I do find it a little odd certain items don’t stack. This doesn’t cause a problem in the bags because you don’t go by slots until full, but instead by weight. However, when you put them into storage, them not stacking become a huge issue.
Gems are the biggest frustration here for me. I can’t keep gems until I need to use them effectively unless I carry them. When you die, you lose them. Obviously keeping these in storage is much safer, but them not stacking (and maybe this is intentional so you can’t keep gems very easily) is very frustrating as a player.