The armor defense values are, I think, in fight.cpp. It might be under damagemod or something similarly named.
Weapons are referenced, unfortunately, all over the place. LCS is, to its detriment, extremely un-encapsulated and procedural (despite that it's really a good fit for OO). It was originally a small project Toady threw together and was never intended to get as big as it did. Anyway, a few off-hand that I can think of:
commonnames.cpp (or something similar) -- weapon name strings
shops (I forget where off-hand) -- purchasing weapons and ammo
creature.cpp -- initializing creatures with specific weapons
stealth/disguise (sitemode or at least that directory) -- weapons factor into getting spotted
My best advice is to do a search across all the source files for WEAPON_, that will net pretty much all the mentions. That's how I'm able to cope with it. 
And certainly no objections to adding flavor text (or other content even -- it's not really my baby or anything, I only seem to be in charge because I'm the main person who works on it. I think the first change I did to get my feet wet was to add new weapons.). Let me know if you want to be added to the sourceforge project, I guess you need to be on the project to make commits.
[ March 03, 2008: Message edited by: Jonathan S. Fox ]
[ March 03, 2008: Message edited by: Jonathan S. Fox ]
[ March 03, 2008: Message edited by: Jonathan S. Fox ]