You don't know what your opponent has. That a flush draw is possible does not mean you should put your opponent on a flush draw. Even if your opponent played nothing but suited hands (and never AKo or pocket pairs), the chance of a two card flush draw on a two-tone flop would be less than 1/4. You should put your opponent on a range of hands. When you have a flush draw, you should consider that your opponent might have missed, might have a lower or higher flush draw, etc.
Few hands are only flush draws. They usually come with other ways to improve, sometimes to the best hand and sometimes to a second-best hand. A flush draw with two overcards is usually a slight favorite over one pair (or against AK unimproved). A flush draw with one overcard or a gutshot is usually only a slight underdog. Even a flush draw with no overcards often has backdoor draws to a straight, two pair, or trips.
The situations you mention, in the early game and when you are heads up, are both ones where you should not be risk averse. Usually make the plays which gain chips. If you get all-in as a 3:2 favorite, great. If you make a good semibluff which has a lot of folding equity, and has good chances to win in case you get called, that's good too. You can look for other ways to play which are even better, but you are not going to get situations as good as those on average.
I don't see the sense in playing tighter HU or "counting on made hands more." That is not what tournament theory says to do.
