Weapon Creator shouldn't be adding any "dummys". Matter a fact if you've forgotten to place your "SMOKE" or "BRASS" bones where these things should be emulating from, you'll find yourself putting them in later for guns that need them( I realize sci fi wouldn't)
WC doesn't actually add anything to your mesh...It simply lets you see it the way the fpsc player does during import.
I use WIN3d from Rhinegold, which is a free converter to change x files to 3ds.
Hope ya get your weapons straightened out...I know my first weapon was a pain that I ended up dropping for others once I had this stuff figured out.
If your curious, I'd visit Errants forum for lots of discussions held on weapons.
http://eai.s3.bizhat.com/eai.html