Well, none of that worked. I did another fresh install of SH3, loaded it up, started a career, and had normal deck gun ammo. Quit the game, installed GWX, moved the data folder back where it was supposed to be, started the game, started a career, checked my deck gun, and again 0 ammo. I started multiple careers in different flotillas, different years, all the same result. I don't know what to do other then to play without GWX, which I guess I could do. There's got to be something I'm doing wrong. Either that or my copy of GWX is f**$@#d.
Do you know if there is anyway I can contact the people who made GWX and see if they know what to do? Or am I SOL?
Edit: This time I also did not install SH3 Commander. The only other thing I did was to use JSGME to enable a few of the GWX mods like the 16km terrain and a few others.
Edit 2: I searched the interweb for "GWX 3.0 no deck gun ammo" and found this
http://www.subsim.com/radioroom/showthread.php?t=171809 Apparently I had to man the deck gun and click on the shell to load the first one. Once I did that it showed my ammo. So yippee, I'm on my way to playing SH3 again! Thanks again for all your help bigboy. Now I get to learn how to play SH3 the proper way.