Well, I do understand that – but it would have some undesired effects as well. I would rather not go into details why. Optimally, all items in a subcategory should be within the parent category as well. I will see what I can do about that in a future update.
The “drop-down as checkboxes” layout was suggested before. Something like that will be added for sure. Probably without a search feature, sort of like a “show filter” with a box layout of some sort.