I put the wooden priest mask and one other priest mask (can't remember which one) in a display case in the entrance to my house in lakeview manor, saved my game and left. After many completed quests, i came back to my house to find one mask outside of the display case and the other (the wooden one) nowhere to be found.

Is there a way to find said item that doesn't involve going back to a very old save file?

Open the console (usually the tilde key top left below esc key), first input help "wooden mask". It should return an 8 character ID. Then input player.additem xxxxxxxx - where the x's are the characters shown in the console. Be sure you put that help command in exactly like that including the quotes....

That gives you a new one. I'm not aware of any way to find something that the HF display cases "ate". It's not a great idea to put stuff in them for exactly that reason. There are various ways to add displays to the HF houses, but really, player modded houses are a better idea by far.

Take a look at http://www.nexusmods.com/skyrim/mods/79756/? by Cynndal. And this is http://www.nexusmods.com/skyrimspecialedition/mods/2860/ for SSE.