Changing sprites or bounds will not break saves, since that data doesn't end up in the savefile and is loaded fresh every time you run the game.
However: if you remove or change the IDs of weapon slots, that could break a save, since a custom variant in the save might be set to use a slot that would, at that point, not exist. Other changes to weapon slots should be fine, i.e. if you change it to a different type, that'll be fine, though some older variants might have an invalid weapon slotted into it.