So, it's quite possible this has been documented before, but anyway...
You probably already know that every item has an "ammo" attached to it. Most of them are unused bytes, but some correspond to other things. There's an index of all the ammo slots starting from deku stick and ending with magic bean. After that is the "magic bean popularity" byte, which also corresponds to how many hammers you have. Light arrow amount is linked to tunics&boots, and Nayru's Love amount is linked to swords&shields. Every bottle item is linked to a single unused byte that can be modified with Gerudo Mask RBA. These ammo counts don't actually do anything for items that weren't intended to use them, but at least the bottle item ammo can be displayed using bottle duplication (and others using cheats).
When you have an item in one of the seven "ammo display" slots in the inventory, the game checks the item to determine where in the pause menu to display the number.
For deku stick, fish, and bugs, it chooses the bottom left corner of the deku stick slot. If you have your deku stick ammo and bottle ammo displaying at the same time, the bottle ammo display will overlap the stick ammo display (unless it's only 1 digit, in which case it will only overlap the rightmost digit).
For deku nuts, bombs, arrows, deku seeds, chus, and beans, the display will go where it's supposed to obviously.
For blue fire, the display is interesting. The two digits of the display will be split in two completely different locations on the menu, neither of which are actually overlapping any items. The first digit is sitting on the left edge of the blue border for the item select screen, a few units above the rupee counter. The 2nd digit is sitting at the top of the border just under your 20th heart in the HUD.
For empty bottle and fairy, there doesn't seem to be an ammo display anywhere, but part of the menu will flicker constantly (although sometimes it may not, depending on the value it's trying to display I think). I've seen the flickering turn white when it's trying to display a value of 200 or more (only possible with cheats).
For bomb bag (20) nothing seems to appear, although maybe it's dependent on the value once again (it's obviously linked to a different byte than the bottle items, but I don't know which one).
EDIT: It flickers, but only inside of dungeons.
Here's an example of these glitched displays:
http://i.imgur.com/oDDXJVn.pngIn this case, I RBA'd Gerudo Mask with fish on B to change the "bottle item amount" to 25. I also got an empty bottle in my bombs slot, blue fire in my bow slow, and a fish in my slingshot slot. The fish makes the 25 display appear over my deku stick ammo (notice it doesn't match my real deku stick amount on C-down). The blue fire shows the number 25, with the "2" digit on the left above my rupee counter, and the "5" digit above my magic to the right of my hearts. The empty bottle in the bombs slot makes the screen flicker (although you can't see it in the image very well; it's somewhat covering my bugs and ruto's letter).
