I'm reading up on pot outs and EV in order to make the correct call to call or not.

One of the things is obviously knowing your outs but something I don't understand... Do we ignore the villain's hand when calculating the outs we have? For example in an example I've seen they use the following dealt hand as example:

AT

with a flop of

5K8

For the outs he says: 9 clubs for the flush + 3 Aces = 12 outs

My question is... Shouldn't we take into account that villain can have ace with better kicker so the above will give us an overestimates value for pot odds?

Similar to let's say we would have KT instead of AT. We would still have 9 outs to the flush but villain might hold the ace so shouldn't we make adjustments for that?

Yes, you must always consider if the "out" gives you a winning hand vs villain(s). Obviously in this case a club gives you the nut flush (unless the unlikely runner-runner str8-flush)

also consider that villain may have 76 and be on the str8 draw....so all your T outs are good.

(Ace outs at 3.... let's discount to maybe 1.5 outs....? but add a few T outs....again maybe 1 ?)

"Outs" are just the cards that can come that improve your hand, based on the reality of all other cards being unknown. If you have ATcc on K58cc, then there are literally 9 other cards in the deck that would give you the nut flush if one of them appears on the board. Your opponent might have one of them in his hand, but then again he might not.
If you knew for a fact that villain had two clubs in his hand (say, 8c 7c), then you'd only have 7 outs to a flush, but you also have 6 outs to a higher pair than his 8.

You're generally pretty safe counting outs when you are drawing to the nuts, but when you have a non-nut draw, you have to be a bit more careful. e.g. T9cc might be drawing to a flush on K58cc, but it could still be drawing to the second best hand (versus the nut flush draw), so you should often be more cautious.
It's also sometimes better to just count clean outs (e.g. you might have 8 outs to an open-ended straight draw, but two of them would complete a flush as well, so you only have 6 clean outs).

With experience, you learn to recognise when you have a strong draw or a weak draw. Most of the time, you only want to put significant amounts of money in the pot if you are virtually guaranteed to win the hand if you 'get there'. e.g. Don't make a habit of chasing the idiot end of a straight, or a low flush. If the pot gets big on 987 and you just have a 6 (or worse, a 5), you're probably still losing if you bink the straight.

It's not just that, villain could have a set already, or two pair, in which case the ace would not give you the best hand. As has already been previously discussed, you should discount non nut outs, especially when you are drawing to a hand as weak as top pair. How passive or aggressive your opponent is will come into play here. Against a rock, who seldom bets without a very strong hand, you could safely count the ace as zero outs, even if the rock could show up with KQ as the bottom of his range. Against a very aggressive or reckless player then you might want to count the ace, at least in part.

yeah you consider raising rather than calling if you think villian has AQ or AJ and you believe he will incorrectly fold enough to make your bluff profitable.

yeah goal is to get all of villians chips in the pot on the flop. you have 60% equity and you got the king so he cant have AcKc.

Villain might also hold 23o and we are way ahead right now.

hero doesn't think villian holds 23o.
hero is awesome or terrible at reading hands and believes villian has AJ+. minus AK of clubs since he has a club. unless dodgy dealer put a extra club in the deck from another packet of cards.