Database

[{"_id":1,"work_week":[{"name":"ponedeljak","work_hours":[]},{"name":"utorak","work_hours":[]},]},{"_id":2,"work_week":[{"name":"monday","work_hours":[{"work_starts_at":1,"work_ends_at":2}]},]},{"_id":3,"work_week":[{"name":"понедельник","work_hours":[{"work_starts_at":2,"work_ends_at":3},{"work_starts_at":6,"work_ends_at":7},]},{"name":"вторник","work_hours":[]},]}]

Query

db.collection.update({"work_week.work_hours.work_starts_at":{$exists:true}},{$inc:{"work_week.$[].work_hours.$[].work_starts_at":-5}},{multi:true})

Result