I don’t think they’re over-represented, just popular for many reasons.
A lot of fairy tales/fables/stories from the past were used to address socio/political issues of the period in a less direct way. Super hero stories are kind of the modern day version of that and allow a vehicle for the authors to tackle real world issues if they so choose.
They offer a classic villain and hero dynamic. It’s the “good and bad” needed in story telling offered right off the bat. Then you could play with so many iterations of that with the main character being the villain, or caught in between the two sides, or being the classic hero. But not many other genres offer you such elements from the get-go.
They allow for a lot of character growth and interesting group dynamics. Teens growing up with superpowers? Shows the maturation of the characters facing growing up with a “supernatural” element. Rag-tag group of outcasts that become loved by the public, outcast who finds a place within an idolized group, the fall of someone once loved by all, the rise of someone who feels they’ve been wronged, etc. etc. are perfect setups.
The setting is (mostly always) modern with mystical components that don’t typically require as much world building as adding in a different kind of magic. World building is still needed, of course, but the general public/government is also much easier to include with the acceptance and knowledge of superpowers vs. “mysterious magic.”
There’s many more reasons, but I think they as well as there being so many ways to explore this genre, make it such a good genre for IF. A lot, for sure, but I have yet to see a game very similar to another on here yet so I wouldn’t say there’s too many.