Why not raise his bet on the flop? He may fold if he's a mad LAG capping with TT, 99 preflop.

He may reraise with AK, KK or AA, in which case you know you are almost certainly beat. If he calls you, you know he has at least QQ. When the Q came on the turn you have even better reason to think you are beat and you could have folded.

But assuming you happened to call his bet on the turn and hit your flush on the river your raise is correct because he can't have a flush with Q set, K set, and AK (non heart), AA (non heart ace) and you're getting odds and those hands might payoff.

However once he re-raises you again on the river, there's no other hand he can have other than the nut flush. Even a very LAGgy LAG would not do it with 4 hearts on the board if they had a set. So I would say 13:1 would not be odds to call.

I think the flop-raise line would have saved you at least 1 BB. I don't think it's it's a discipline issue. I think about understanding the play, getting information on the opponents hand range cheaply, fitting it to the flop texture and looking at the odds.