This was a necessary side effect of making you be able to carry more items than the hotkey count limit. You can still change hotkeys through the inventory menu by selecting the item and then inputing the hotkey change command IIRC.
As for auto assigning hotkeys I believe it doesn’t do this because the game saves hotkeys based on item type. So if you assign a battery to ‘b’ then it will try to assign any new batteries to the ‘b’ key if you pick them up later.