when placing ammo into the tank, it disappears from the UI?
has the following behavior:
-only the first 50 ammo or so disappears?
-the tank can use the ammo when driven automatically
-the tank can not use the ammo when driven manually
-picking up tank will recover the ammo

Yes, this is all correct. The reason is the ammo has been moved into a hidden turret entity that does the actual firing at enemies. I've added an acknowledgment of this behavior to README.md (in my local copy, for the moment). I'm not aware of any good way to "fix" this, however.

After thinking about it I realized the AAI mod was doing the exact same thing, although it only moves/hides 1 magazine at a time instead of 50. I thought it was a bug, but it was less of an annoyance. At the least, I could still check which vehicles were low of ammo and manually fire.

I'm unaware of other mods with vehicles that automatically fire. As you said, this behavior might be unavoidable.

The reason for moving 50 at a time is to allow the code that checks for missing ammo to run less often, so the mod uses less CPU. I originally moved 10, but then changed the code to only check on every 5th frame, so wanted a corresponding reduction in the total downtime by having them run out less often. I could make both numbers configurable. I could also look at providing some other form of low-ammo notification.