Removing the ability to use tools on pick-up resources is imho just as questionable as the removal of the precision split for stacks.
Using tools on pick-ups has been around since early access. I’d even bet that it was a thing since day one. It has been around for so long that it was assumed to be an intended feature (although, precission splitting was a an intended feature, too…).
So unless it is your intended goal to make the game more annyoing to play, PLEASE remove this “bug fix”.