More than that, I think two or so an episode. There are three in the first (Mrs Hudson, Angelo, and Mycroft), and that's if you count Angelo's shipping of Johnlock and Sherlock's clumsy attempt to let John down gently as one joke. Oddly enough, I can't find a tally, so I'll keep one on my next marathon.

The jokes are good - anything that causes Freeman to act one of his nine or so flavors of exasperation is automatic comedy gold. I'm just complaining about the frequency.

they did it rather inconsistently

I think the mood dictates that. A Study In Pink is meant to show Sherlock's abilities, so we can exclaim "Fantastic!" in chorus with John, which is why we get both clue highlighting and expospeak. Baskerville is about Sherlock losing it a little, so making things less clear helps.

I agree that the characters are sometimes dense. In Reichenbach, Sherlock misses or takes forever to get nearly all of Moriarty's hints, though a large part of it is probably playing dumb. (Moriarty's last move genuinely surprises him, but he didn't phone that one in.) My personal theory for his abysmal stupidity in A Study In Pink is that he starts out incapable of any thinking while distracted (e.g. by Anderson's face) and that improvement in this area is one of the benefits of having a sidekick-caregiver-sober coach.