Items set to hotbar still there even after I have put that item into storage

[Justus]

could hotbar detect and remove its stack automatically when its related items are not in the inventory anymore.

 

[Sangemdoko]

That's how the basic hotbar works. If you want a differente functionality check out the "equipment" hotbar or the inventory mirror hotbar in the feature scenes.
If none of them suit your needs you can make your own custom hotbar using those three as inspiration