That IS an issue.
MSs build have +8 accuracy with a basic pistol on the edge of vision, which translates in 98%.
MBD have +2, which is just 74%.And it blocks EE.
And missing almost quarter of your shots can't be called a little.
Post above. Also I would add that with crappy accuracy hitting targets at the edge of FOV (or outside of it) is really crappy.
At LOS you lose 26% of your DPS on any build without EE. No, that's not a small amount. But it also doesn't always apply, because you aren't always shooting targets at LOS. I don't care about it for these tables, I already said at the start that I'm not going to take that into consideration, it would be too large of a variable anyway for my purpose.
Having tactical, active, or passive defense makes a big difference. "Not a major effect" in your opinion can translate into not being able to kill Cyberdemon, for example, IMHO.
Two comments.
For monsters:
The only monsters with more than 3 armor are bosses, and, with the exception of AoD (who you can't use pistols against), they don't go any higher than 5. So for bosses, yes, it will have an effect. Overall... not so much. I'm not looking at little corner cases in these tables. Calculating DPS versus 2 armor cause slightly less than 25% drop in DPS (it has a lower effect than the 25% accuracy penalty does).
For players:
I'm assuming you're firing the entire clip and then reloading afterward. How you end up playing will lower (or raise) the actual DPS. As will if you are firing at a target out of line of sight, if you have a modded weapon, if you have other traits that effect reloading and fire time, etc... All of these things affect DPS, but these tables are just a base representation of what to expect, and I'm making certain assumptions which I know will not possibly always hold true in an actual game. Same goes for my Expected Level for each Floor tables.
Ammo can be a problem at some point. Pure DPS statistics won't tell you that instead of using four bullets to kill something you can use just two.
(Highlighting mine)
And these are nothing more than pure DPS statistics. So it's a caveat to the results, not a problem about the results.