I've been using Marksman spec on my hunter so my pet almost becomes a non-issue. From what I saw, I could probably do a little bit higher combined DPS (hunter+pet) using Beastmaster, but the reality is that most ppl judge you on what DPS YOU produce and don't even look at the pet.
aka, when I was testing awhile ago (my gear was pretty crappy), in beastmaster spec, I was doing about 9k dps and my pet about 4k... a total of 13k. In the same gear but in Marksman spec, I was doing about 10-11k and my pet was doing about 1k - a total of 11-12k, a little lower total then I was doing beastmaster... AND YET... people saw MY dps and I got zero complaints... unlike the few times when I was beastmaster and ppl would point out my dps was <10k... Yep, it was... but if me and my pet left, that would have been a drop of 13k (again - yes that is low too, crappy gear - just an example)
So... at the end of the day, when it comes to instances, I don't even care what my pet dps is... in PvP, that's different of course, cause then it's not only what dps they can do, but other effects as well... can they effect the play of the target?