Alright, so effective stacks are 40xbb. You didn't say what the initial two raises were, so I will assume min-raises. You still would be able to get nearly your entire stack in pre-flop.
Villian raises to 2xbb ($0.50)
[everyone folds to you]
SB [Hero] raises to 3xbb ($0.75)
[BB folds]
Villian pots it to 10xbb ($2.50)
SB [Hero] calls 10xbb ($2.50)
Pot is 21xbb ($5.25), effective stacks are 30xbb ($7.50), flop SPR ~= 1.5
It's a get it in situation, even if those were min-raises. But, note that you could have made it 31xbb pre-flop (basically all-in, which is a good spot to be in omaha with aces). The more of your stack you can get in (pre-flop) with aces, the happier you are. People caution being slow because 3-betting can give away your hand and that's bad when deep. If you 3-bet AA out of position when 200xbb deep and get called, you're in horrible shape if you don't hit an ace.
I can't really explain his call. It happens. People call, in this game. You'll see worse beats. He still has almost 13% equity on that flop. I think my worst beat was flopping the nut straight against bare Aces (he had no draws). He was 4% to win, and did. The board ran runner-runner trips to give him a full house. Can't let it get to you. Just play within your
bankroll.