In some cases, they probably do. But there are certain pitchers who get more than their share of strikes called because of their reputation. Mariano got something like 20% more strikes called than he should have. I don't think umpires do that intentionally, I think it's mostly due to confirmation bias.
Also, umpires are more likely to call a ball a strike on a 3-0 count than they are at other times. With the count now 3-1, how often do hitters who should have received a walk go on to make an out or even get a hit, which affects their and the pitchers' BB stat.
At any rate, whether the calls even out or not really shouldn't be a consideration. It doesn't change the amount of subjectivity that goes into those stats.