app.js

const input = {
    dishonest_total: [3,6,2,7,1,9],
    customer_inn_and_name_list: ["aa", "bb", "cc", "dd", "ee", "ff"],
    dishonest_rest:  [5,1,6,1,4,1],
    dishonest_true:  [0,3,3,8,1,1]
}

const merged_array = []
for(var i = 0; i < input.customer_inn_and_name_list.length; i++) {
  merged_array.push({
    customer_inn_and_name_list: input.customer_inn_and_name_list[i],
    dishonest_total: input.dishonest_total[i]
  });
}

merged_array.sort((a, b) => a.dishonest_total - b.dishonest_total)

const output = merged_array.reduce((arr, val) => {
  if (!arr.customer_inn_and_name_list) arr.customer_inn_and_name_list = []
  if (!arr.dishonest_total) arr.dishonest_total = []
  arr.customer_inn_and_name_list.push(val.customer_inn_and_name_list);
  arr.dishonest_total.push(val.dishonest_total);
  return arr;
}, {});

console.log(output);