Usual disclaimer: I am not a lawyer and in this site questions about these issues have to be always taken as ideas, thoughts or experiences, never as technical advice.
That said, first of all, certainly words in themselves are not trademarked per se. I very much doubt that the word "superhero" or its variants could even be trademarked. And even if they were, I very much doubt that such trademarking would make any sense in any judicial dispute.
Second, however, yes, character names can be and often are trademarked. For instance, in a quick search, you can find an entry related to Marvel's Cyclops or Marvel's Magneto. And, to be honest, even if they didn't trademark their characters, they would still have a possible claim over their names - you own the rights over the things you create even without registering them.
Sure, if you take the name of a character and change it enough, you might be safe from issues regarding the trademark of the original name. The practical problem is how much is "enough". It is something that can't be determined a priori. Therefore, there is always risk.
Of course, some big companies only bother going after big enough contenders, i.e. they won't pay much attention until your games are successful enough to get into their radars. Others, however, are pretty strict and tend to cause trouble even for the smaller unknown developers, or even for modders and fans. Nintendo, for instance, has already took down a fan-made non-profit learning project: http://ca.ign.com/articles/2015/03/31/nintendo-takes-down-super-mario-64-hd-fan-project. It means that, again, there is risk.
Whether those risks are worth taking, is something that you and only you can decide. But those risks are, often, enough of a burden. Specially for independent developers. You have to consider that the problem of being sued is not only loosing, but even before that, wasting time and resources on the matter. Time and resources that are, of course, far more costly to you than to big companies like Marvel and DC.