WOW!
Welcome aboard.
GWX removes AP and AA shells, because historically they didn't use them. Merchants and destroyers have no armor. The smallest ship to carry armor is the light cruiser, and if you really want to take your 8.8cm gun up against six 6" (15cm) guns, be my guest.
One of the first rules I learned is to always keep a copy of the stock game handy in a special folder so I can grab any unmodded files I might need in the future.
I've forgotten how to restore the stock ammo files, but rest assured someone will be along soon with that information.