Who do you think will figure out that they're a couple first? I'm betting on Espo.
Martha.
(FWIW, I think that the guys have been assuming that they are lovers for ages now, they just have not been able to prove it.)
I think that Castle's reasons for discretion have more to do with wanting that little thrill of the secret rather than any other reason. He loves her and his mother already knows that; so when he starts not coming home over night on a regular basis she will know right away. (Mind you, NOT having his mother embarass Kate about it is probably one of his reasons as well; Martha doesn't have much of a filter, and he doesn't want to scare Kate off before she fully adapts to the new situation.)
THE big question of the season, I think, is when will she break down and actually say the L Word? I don't think it is any accident that she has not done so on camera. (Apparently she DID tell Rick about the resignation off-camera; otherwise I don't know how he would have known about it by that morning, since he had not checked his messages all night.) The other big question of the season is what exactly Kate is doing that is putting those really goofy grins on his face every time they allude to their intimate moments -- there have been comic hints for a LONG time now that she is rather adventurous in that regard, and I'm waiting for some sort of running gag about Castle not being able to keep up with her.
Also, speaking of not checking his messages, the situation with hiding Kate meant that his not answering Alexis' distress call was glossed over. I don't doubt that that will come back to haunt him sometime soon, because Alexis is definitely used to being at the top of his priority list.
PS: IMO, the most pivotal moment in this series wasn't in either of the two big ones that most people mention:
Knockout or
Always. I think it was the point in
Sucker Punch when she chose to shoot to kill Coonan. She was shooting him at essentially point-blank range; she could have easily chosen to shoot to disable rather than to kill, but she chose to kill him, even though she regretted the ramifications moments later and desperately attempted CPR. At the moment that she pulled the trigger, whether she realized it or not at the time, she chose Castle over her need for revenge.