index.js

var Sequelize = require('sequelize');
var sequelize = new Sequelize(
    'mysql://root:root@localhost:3306/sandbox',
    {
      dialect: 'mysql',
    }
);

var User = sequelize.define('User', {
    name: { type: Sequelize.STRING },
});
var Resource = sequelize.define('Resource', {
    name: { type: Sequelize.STRING },
});
var Booking = sequelize.define('Booking', {
    name: { type: Sequelize.STRING },
});

BookedResource = sequelize.define('BookedResource', {
  id: { type: Sequelize.INTEGER, primaryKey: true, autoIncrement: true },
  ResourceId: { type: Sequelize.INTEGER },
  BookingId: { type: Sequelize.INTEGER }
});

User.hasMany(Booking);
Booking.belongsToMany(Resource, { through: { model: BookedResource, unique: false}, foreignKey: 'BookingId' });
Resource.belongsToMany(Booking, { through: { model: BookedResource, unique: false}, foreignKey: 'ResourceId' });

sequelize.sync({force: true})
.then(() => {
  return Sequelize.Promise.join(
    User.create({"name": "Armando"}),
    Booking.create({name: "booking yowza"}),
    Resource.create({name: "item1"})
  )
  .spread((user, booking, resource) => 
    Sequelize.Promise.join(
      booking.addResource([resource, resource]),
      user.addBooking(booking)
    )
  )
  .spread((booking, user) =>
    Sequelize.Promise.join(
      User.findAll({include: [{model: Booking, include: Resource}]}),
      User.findAll({include: [{model: Booking, include: Resource}], raw: true})
    )
  )
  .spread((users, usersRaw) =>
  {
    console.log(users.map(u => u.toJSON())[0].Bookings[0].Resources);
    console.log(usersRaw);
    sequelize.close()
  })
})
.catch(err => {
  console.log(err);
  sequelize.close();
});

/*
Output:

Regular query (undesirable behavior, since Resources.length=1)
[ { id: 1,
    name: 'item1',
    createdAt: 2017-07-01T23:09:28.000Z,
    updatedAt: 2017-07-01T23:09:28.000Z,
    BookedResource: 
     { id: 2,
       ResourceId: 1,
       BookingId: 1,
       createdAt: 2017-07-01T23:09:28.000Z,
       updatedAt: 2017-07-01T23:09:28.000Z } } ]

Raw query (desired outcome, since both Resources come up with the two distinct BookedResource id's):
[ { id: 1,
    name: 'Armando',
    createdAt: 2017-07-01T23:09:28.000Z,
    updatedAt: 2017-07-01T23:09:28.000Z,
    'Bookings.id': 1,
    'Bookings.name': 'booking yowza',
    'Bookings.createdAt': 2017-07-01T23:09:28.000Z,
    'Bookings.updatedAt': 2017-07-01T23:09:28.000Z,
    'Bookings.UserId': 1,
    'Bookings.Resources.id': 1,
    'Bookings.Resources.name': 'item1',
    'Bookings.Resources.createdAt': 2017-07-01T23:09:28.000Z,
    'Bookings.Resources.updatedAt': 2017-07-01T23:09:28.000Z,
    'Bookings.Resources.BookedResource.id': 1,
    'Bookings.Resources.BookedResource.ResourceId': 1,
    'Bookings.Resources.BookedResource.BookingId': 1,
    'Bookings.Resources.BookedResource.createdAt': 2017-07-01T23:09:28.000Z,
    'Bookings.Resources.BookedResource.updatedAt': 2017-07-01T23:09:28.000Z },
  { id: 1,
    name: 'Armando',
    createdAt: 2017-07-01T23:09:28.000Z,
    updatedAt: 2017-07-01T23:09:28.000Z,
    'Bookings.id': 1,
    'Bookings.name': 'booking yowza',
    'Bookings.createdAt': 2017-07-01T23:09:28.000Z,
    'Bookings.updatedAt': 2017-07-01T23:09:28.000Z,
    'Bookings.UserId': 1,
    'Bookings.Resources.id': 1,
    'Bookings.Resources.name': 'item1',
    'Bookings.Resources.createdAt': 2017-07-01T23:09:28.000Z,
    'Bookings.Resources.updatedAt': 2017-07-01T23:09:28.000Z,
    'Bookings.Resources.BookedResource.id': 2,
    'Bookings.Resources.BookedResource.ResourceId': 1,
    'Bookings.Resources.BookedResource.BookingId': 1,
    'Bookings.Resources.BookedResource.createdAt': 2017-07-01T23:09:28.000Z,
    'Bookings.Resources.BookedResource.updatedAt': 2017-07-01T23:09:28.000Z } ]
*/

This can probably solve the issue

User.hasMany(Booking);
Booking.belongsToMany(Resource, { through: { model: BookedResource, unique: false }, foreignKey: 'BookingId' });
Resource.belongsToMany(Booking, { through: { model: BookedResource, unique: false }, foreignKey: 'ResourceId' });
Booking.hasMany(BookedResource);
BookedResource.belongsTo(Resource, { foreignKey: 'ResourceId' });
BookedResource.belongsTo(Booking, { foreignKey: 'BookingId' });

sequelize.sync({ force: true, logging: false })
    .then(async () => {
        const [user, booking, resource] = await Promise.all([
            User.create({ "name": "Armando" }),
            Booking.create({ name: "booking yowza" }),
            Resource.create({ name: "item1" })
        ]);
        const [booking_1, user_1] = await Promise.all([
            booking.addResource([resource, resource]),
            user.addBooking(booking)
        ]);
        const [users, users1, usersRaw] = await Promise.all([
            User.findAll({
                include: [{
                    model: Booking, // belongsToMany <---------------------
                    include: [{
                        model: Resource,
                        through: { attributes: [] }
                    }],
                }]
            }),
            User.findAll({
                include: [{
                    model: Booking, // hasMany <---------------------
                    include: [{
                        model: BookedResource, // belongsTo <---------------------
                        // attributes:['id'], 
                        include: [{
                            model: Resource,
                        }],
                    }],
                }]
            }),
            User.findAll({ include: [{ model: Booking, include: Resource }], raw: true })
        ]);
        // console.log(users.map(u => u.toJSON())[0].Bookings[0].Resources);
        console.log('users', JSON.stringify(users, null, 2));
        console.log('users1', JSON.stringify(users1, null, 2)); //<---- modified findAll
        // console.log(usersRaw);
        sequelize.close();
    })
    .catch(err => {
        console.log(err);
        sequelize.close();
    });

Output:

users [ 
  {
    "id": 1,
    "name": "Armando",
    "createdAt": "2021-05-19T11:02:31.844Z",
    "updatedAt": "2021-05-19T11:02:31.844Z",
    "Bookings": [
      {
        "id": 1,
        "name": "booking yowza",
        "createdAt": "2021-05-19T11:02:31.846Z",
        "updatedAt": "2021-05-19T11:02:31.942Z",
        "UserId": 1,
        "Resources": [ // belongsToMany
          {
            "id": 1,
            "name": "item1",
            "createdAt": "2021-05-19T11:02:31.846Z",
            "updatedAt": "2021-05-19T11:02:31.846Z"
          }
        ]
      }
    ]
  }
]
users1 [
  {
    "id": 1,
    "name": "Armando",
    "createdAt": "2021-05-19T11:02:31.844Z",
    "updatedAt": "2021-05-19T11:02:31.844Z",
    "Bookings": [
      {
        "id": 1,
        "name": "booking yowza",
        "createdAt": "2021-05-19T11:02:31.846Z",
        "updatedAt": "2021-05-19T11:02:31.942Z",
        "UserId": 1,
        "BookedResources": [ // hasMany + belongsTo -> need to reformat array
          {
            "id": 1,
            "ResourceId": 1,
            "BookingId": 1,
            "createdAt": "2021-05-19T11:02:31.989Z",
            "updatedAt": "2021-05-19T11:02:31.989Z",
            "Resource": {
              "id": 1,
              "name": "item1",
              "createdAt": "2021-05-19T11:02:31.846Z",
              "updatedAt": "2021-05-19T11:02:31.846Z"
            }
          },
          {
            "id": 2,
            "ResourceId": 1,
            "BookingId": 1,
            "createdAt": "2021-05-19T11:02:31.989Z",
            "updatedAt": "2021-05-19T11:02:31.989Z",
            "Resource": {
              "id": 1,
              "name": "item1",
              "createdAt": "2021-05-19T11:02:31.846Z",
              "updatedAt": "2021-05-19T11:02:31.846Z"
            }
          }
        ]
      }
    ]
  }
]

User.create({ "name": "Armando" }),
            Booking.create({ name: "booking yowza" }),

Olá, eu fiz dessa forma e funcionou, obrigado!