Damage bonuses are a flat +x damage on each hit, not a modifier on the weapon's stats.
Damage formula has a number of things that factor in besides the damage on the weapon and your strength, which is what's affecting how hard you hit with your KD.
I'm not sure if anyone really KNOWS the p99 formulas for dw and da, but I'm pretty sure the wiki has the stock emu formulae on it somewhere.
http://wiki.project1999.org/index.php/Game_Mechanics