As Blue and Simon's correspondence continues, they come to view superheroes as a symbol for what it's like being secretly gay. Around Halloween, Blue mentions that he always dressed up as a superhero for Halloween as a kid. Blue and Simon interpret their "superhero identities" as who they are in their emails to each other (out and happy to be gay), while their "civilian identities" are who they are in their day-to-day lives (closeted). Bram and Simon's experiences coming out then serve to merge their two identities into one that's far more comfortable than switching between two identities as superheroes do.
Superheroes Quotes in Simon vs. the Homo Sapiens Agenda
“I completely see the appeal of being someone else for the evening (or in general). Actually, I was a bit of a one-trick pony myself when I was little. I was always a superhero. I guess I liked to imagine myself having this complicated secret identity. Maybe I still do. Maybe that's the whole point of these emails.”