Part of the trouble that it sounds like you're running into is that comics are a visual medium; the transition of superheroes to text is almost always a slightly awkward one because you suddenly lose a sense- it's like your audience has abruptly been struck blind.
Comics, when dealing with a Cast Herd, tend to rely on iconic design cues- Blue-Red-Yellow plus stylized-S-in-Shield equals Superman, Pointy-Eared Cowl plus Scallopped Cape plus Bat-Logo plus Subdued Colour Scheme (... typically >.>) equals Batman, Blue-Red-Black plus Web-flavoured design plus weird Mask-Eye-things equals Spider-Man, and so forth.
I'd suggest finding a literary equivalent that works for you- for example, a consistent descriptor that you can use for the character in question, even if they change nom de guerre or costume. Done subtly, your readers might never notice it, but nevertheless find that they don't have much trouble telling the characters apart.
TEST
I'm writing a superhero story and the cast is going to be pretty massive. However, I'm worried audiences might get confused by it. While the trope on its own can be confusing at times, there's also the fact that there are Legacy Characters and Meaningful Renames throughout as the story progresses. As in, characters will take codenames of older characters or switch codenames that fit them better, and sometimes you have both (a character switches their codename and another character takes the discarded name).
These tropes are often present in the world of superheroes, hence why I included them. Is there any suggestions to avoiding audiences being confused by this, or is it inevitable?