Fencing actually has 41 women's programs throughout all 3 divisions, and all 3 divisions compete in one national championship. Since the 90's they've actually been coed championships, but for some reason the NCAA lists them as separate mens and womens, rather than "mixed".
Skiing has 38 women's and 34 men's by my count, but again is a sport that is competed in as coed, so assuming there's at least 2 schools that have only men's programs (didn't actually take the time to look), that's why they make the cut. Seems like upstart sports where competition is actually individual have been able to use this co-ed moniker as a way of sort of gaming the system to meet requirements.
Don't really know what to say about gymnastics. Does anyone have a link to the official rules of how NCAA sports become NCAA sports? Maybe there's a loophole of some sort? Something about how if one gender has the sport, then the other has to be offered it (or it's equivalent, in the case of say softball), assuming there's interest in it? Or maybe the 40 programs is M&W combined? Not really sure.