Flexible serialization using SOs and DTOs

Item.cs

[Serializable]
[JsonObject(MemberSerialization.OptIn)]
public class Item {
    [JsonProperty]
    public string Id;
    
    // ... other stuff
    
    /// <summary>
    /// This only needs to be implemented for *mutable* serialized properties.
    /// Properties that already exist on the ScriptableObject will be cloned
    /// during deserialization and are never persisted.
    /// </summary>
    public virtual void PopulateFromJson(JObject json) {
    }
}

ItemAsset.cs

[CreateAssetMenu(fileName = "Item", menuName = "Scriptable Objects/Items/Item")]
public class ItemAsset : ScriptableObject, IItemAsset {
    // ... all your properties
    
    public virtual Item CreateItem() {
        return new Item {
            // copy properties from the SO into the instance
        };
    }
}

ItemConverter.cs

using System;
using Newtonsoft.Json;
using Newtonsoft.Json.Linq;
using Zenject;

/// <summary>
/// Items by default only serialize their ID, which we can map to a scriptable
/// object in the ItemRegistry. Any mutable properties beyond that template
/// must be deserialized in Item.PopulateFromJson.
/// </summary>
public class ItemConverter : JsonConverter<Item> {
    [Inject] protected readonly ItemRegistry _itemRegistry;

    public override bool CanWrite => false;

    public override Item ReadJson(
        JsonReader reader,
        Type objectType,
        Item existingValue,
        bool hasExistingValue,
        JsonSerializer serializer
    ) {
        var json = JObject.Load(reader);
        var id = json["Id"].Value<string>();
        var newItem = _itemRegistry[id].CreateItem();
        newItem.PopulateFromJson(json);
        return newItem;
    }

    public override void WriteJson(JsonWriter writer, Item value, JsonSerializer serializer) {
        throw new NotImplementedException();
    }
}

ItemRegistry.cs

/// <summary>
/// A collection of all ItemAsset ScriptableObjects, keyed by their ID, which is also their filename.
/// </summary>
public class ItemRegistry {
    protected Dictionary<string, ItemAsset> _registry;
    public ItemAsset this[string id] => _registry.GetValueOrDefault(id);
    
    // I use Zenject to populate this singleton, but you can just as easily use Resources.Load
}