Well, you do need to count the times you're sucked out on. If you have a large enough sample of AQs, the times you win should make up for the times you get sucked out on. How many AQs hands do you have?

I thin you can ignore the money you put in when you couldn't lay it down if you have acknowledged your mistake to yourself and don't make it again in the future. You have to be honest with yourself though.

Well I lose money with AQs and AKs too, but win with AKo and AQo. Provided your AQ's make $$$ overall from EP both AQs and AQo should go on your core list. If they only make money from LP then there might be a case for dropping to your marginal list (at least until you find out how to play them better)

It's not a sign that AQs is worse than AQo (it clearly can't be). But it may well be a sign that you are overplaying AQs (as in too often and/or too strongly). The other possibility is that, because only 1 in 4 AQ hands is AQs you may have a small enough number in your DB that the results aren't reliable. Go through each time you have played it and try and work out your EV assuming no suckouts (either for or against you) and 50% on any coinflips. See how the hand looks now..