I think the biggest thing about this is if you check the flop, the hands you beat are more likely to be either more scared of a turn bet (ie the cards ensign lee listed + Q/K/A), or else hit a set and get you into the same trouble you are in if they flop it.

However on the flop, he might check/call with 33 and 66, and maybe 77-99. It's not a bad thing if he folds the missed pocket pairs. And like izybx wrote - he lets you know if he hit a set, ie check/raising the flop or turn. Maybe you can squeeze another $1 of ev by checking the flop behind from 77-99, but I don't think it's worth it.