That puzzle with 28 3's got dinged by the reviewer for that, but it was an oh-so-cute novelty theme, and obviously the fill didn't much matter. When you look at that puzzle, you find ONO, OTT, RTE, CEO, ALT, EEL, ADA, MTA, ORK - pretty crappy fill IMO. So if you come up with a theme that's as clever as that, no one's going to worry about how many three letter words you have (or in this case what they are).
Sometimes the theme forces a high 3-letter word count, and that's often forgiven. But I think the point is, you should design your grid to minimize the number of 3-letter words given the theme set you're working with.