By the start of Spidey 3, Peter is not yet a full-time employee of JJJ. Thus, everyone's points above hold true, that JJJ and most of the Bugle staff don't know about Parker's personal life outside of him snapping Spidey pix for them.
The only one there at the Bugle who would be even slightly hip would be Robbie, esp. given the sidelong glance he gave Peter in Spidey 2 when he said "I heard Spider-man was there...". In the books, Robbie had a great intuition concerning Peter and his relationship to Spidey, probably enough to connect the dots for himself. But given Robbie's integrity, he's not gonna rat Pete out to Jonah.
On another note, John Jameson DID know about MJ's past with Peter, and is no doubt fully aware of her feelings for him. I wouldn't be surprised if he didn't put two and two together to surmise that the same 'pal' that MJ referred to as a 'jerk' in Spidey 2 was the one she ran off to. Either way, I doubt John is hurting too deeply, I mean, he's a #@%@$@#n astronaut for cryin out loud!
That said, Jonah barely pays attention to Hoffman half the time (if he did, he'd realize that he's Raimi's brother and is probably in the closet), so no doubt he's gonna be all into some punk kid photographer.
"I never promised a job! Meat! I'll send you a nice box of Christmas meat!"
"Freelance! Best thing for a kid your age!"
