I can't seem to reproduce this issue with a fresh config (gzdoom.cfg) when I load SmoothDoom first and then JPHUD - the ammo display always draws near the right edge of the screen with no cut off, no matter what aspect ratio or scaling factor I choose.
FWIW the version of SmoothDoom I have is the latest one in this thread: https://forum.zdoom.org/viewtopic.php?t=45550