Thank you for all your input guys! I'm still at it, working on the HUD.
Unfortunately, I gotta say option 2 is out. During all my testing, I forgot to go into a dungeon and didn't realize the dungeon map would cover up the rupee counter. Silly oversight, indeed, and my apologies for the mistake.
Alternatively, why have a rupee counter in the item menu at all?
Rupees are only relevant inside shops and you already have a rupee counter in your HUD.
There's no reason to see them in the item menu that I can remember.
Well, the HUD you see while walking around is what I'm trying to make nicer. Having 20 hearts, a rupee counter, Slot B and Slot A, makes it feel cluttered. With only 1 tiles worth of space remaining, there isn't much room for layout improvement.
So that's why I'm considering removing the rupee counter from the HUD, and having it in the inventory screen only. My thought was similar to what you and retroverse said, that there isn't much need for the rupee counter to be available at all times. With it gone from the HUD, it's more aesthetically pleasing, but you'll have to open the inventory screen to check your rupees. My hope is that this doesn't become a hassle.
There is still room for improvement, so all feedback on this will help immensely!