As soon as I read ILRR's post about Hawkes discovering them, I was all, "I did that! In one of my fics, I did that!" XD
As for answering my own questions, I agree with several people on here, that they're still exploring how they feel about each other and getting to know one another. I think "Stealing Home" and "Charge of This Post" would be turning points for both Flack and Lindsay, though, in making them realize 'hey, maybe I like him/her more than I thought.'
I think Danny would catch on quickly, mostly because Flack's his best friend. Also: Danny flirts with Lindsay a lot and since Don/Lindsay/Danny is my OT3, I can so see Danny getting all angsty over this and finding out in a most unsavory way. Then trying to beat up Flack. Stella, of course, would know -- she's no ordinary superwoman. And maybe Sid Hammerback, because he's pretty much the man.