1. will be fixed
2. I don't have much experience with that, but I haven't changed anything... if it works with OXC/OXCE, it should work with OXCE+ too
3. In the inventory, the search also considers weapon category... so you can search for everything that is "underwater" or "plasma" or "fire damage".
Bone club has following categories, and matches "w" from "Underwater"
STR_BAT_CAT_STUN: "Dmg: Daze"
STR_BAT_CAT_UNDERWATER: "Underwater"
STR_BAT_CAT_0G: "0-G"
STR_BAT_CAT_MOSTLY_HARMLESS: "Mostly Harmless"
Also it ignores alien artifacts... so if you search for heavy plasma, but you don't have it researched yet, it won't find it.
4. It's not a 100% fix either... but I guess better than what we have now... it will just be harder to explain why it doesn't work in some cases... I'll add this in the (near) future.