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Of course J. Jonah Jameson knows that Peter Parker is Spider-Man. Only an idiot wouldn’t realize it, and Jonah is far from an idiot. You don’t become managing editor and publisher of one of the largest papers in New York by being an idiot. (Or maybe you do. Could explain a few things about the Bulletin. Honestly, letting Urich, who is by far the best reporter on the superhero beat, go is a level of stupid Jonah can’t even begin to fathom.)
But seriously, his identity was obvious from the moment he showed up trying to sell pictures that were far too good to be taken without intimate access to the hero. You could try and write it off as Parker just being friends with the hero, but that only works if you completely ignore the angle of Spider-Man’s webs. Once you look at those, it quickly becomes obvious that Spider-Man is using the webs to remotely operate the camera’s shutter. Which is really quite impressive. Jonah does kind of wonder how long it took him to work out how to do that. It’s a good thing for Parker that they live in the age of digital photographs, because the thought of how much film the kid would have wasted otherwise kind of makes Jonah shudder.
Plus, the kid’s secret identity is like the worst kept secret in all of New York. Jonah’s honestly surprised that there are any reporters in the city who don’t know it. Or maybe they do, but are just keeping uncharacteristically quiet about it. New Yorkers take care of their own after all. And Spider-Man is certainly one of their own. He’s been that since the day he saved the city from the Green Goblin, and everything that followed.
The thing is… if the New Yorkers are protecting Spider-Man, then well, Jonah’s just as complicit as the rest of them. As previously stated Jonah knows that Peter Parker is Spider-Man. And he doesn’t say anything.
Part of his reporter’s soul shrieks in agony at that. The idea of having a scoop that huge and doing nothing about it just feels wrong . But every time he sits down to write out the story that will reveal it all he can’t. He just… can’t. Try as he might the words just won’t come. He just can’t bring himself to rip off the kid’s mask. Well, at least not that mask anyway. The kid had some other masks that he really needs to rid himself of. But Jonah really doesn’t have any right to speak there. After all, Jonah knows a thing or two about wearing a mask.
In many ways nearly everything Jonah shows to the world is a mask. The loud mouthed reporter? Mask. (When he was a kid he was a pretty quiet person. He had to train himself to be this brash.) The hard-ass editor who doesn’t give two shits what his reporters have to do to get the story? Mask. (Jonah does have some ethics. There are lines even he won’t cross.) The cape-hater who thinks all superheroes are menaces to society? Mostly a mask. (He still thinks that heroes should have some accountability. But even he’ll admit that as long as there are supervillains they need superheroes to fight them.) About the only side of himself that Jonah lets show that isn’t a mask is his pride in John. (His boy is an astronaut! How cool is that?)
Jonah’s biggest mask though, the one he can’t let slip no matter what, is that he does not care about Peter Parker. That mask is the only thing that keeps him from shrieking in terror every time Spider-man dives headlong into a fight against impossible odds. It is that mask that helps him cling to the idea that he’ll never write the story revealing Parker’s identity.
Because he will write it one day. He knows in his soul that he will. And when he does, it will be an obituary.