There are thought bubbles in Gerry Conway's and Wein's and so on, but the significant moments with MJ (such as the Epilogue at the end of ASM#122) has her silent. And it's not a big deal there.
The most significant thought bubble MJ had was in her last issue with Wolfman where she thinks aloud about her parents' divorce (which unintentionally laid the seeds for Mary Jane's transformation and character development, setting her on the road to marriage).
In any case the period you are talking about i.e. MJ blatantly wondering who Spidey is, is a fairly small part of her publication history, little more than fifty issues far less than 100, and then she was removed out of the titles for 40+ issues before returning in Roger Stern's run, around ASM#238. Stern's run already reconfigured with her backstory (albeit not the element of her knowing Peter's identity), but nothing really contradicted it. The one issue where Stern delves into Mary Jane's psyche, in fact the issue that really did so, is ASM #246 "The Daydreamers" and if you read that, it works if you get that MJ knows Peter is Spider-Man just as well as if you think she doesn't. Then Tom Defalco came in 10 issues later with the reveal in ASM#259, and more or less Mary Jane has remained the character she was in ASM#259, having never gone to any earlier period than that.
So in the long run, it's not a problem. The retcon doesn't fill every gap but in terms of Lee-Romita era, the epilogue of Night Gwen Stacy Died, a lot of Conway's run. It does that well. And for the little that there isn't, it's not such a big stretch that it sticks out.
More importantly, on a character level, even when she was dating Peter, she never really had too many issues with the Spider-Man side of things. She didn't hate Spider-Man unlike any of his girlfriends from before. So there was never any big significant moment where Peter being Spider-Man was an issue with their relationship. So there's not even a tiny elephant in the room to address.