I think it depends on the person you are up against. I have a good friend that plays no fold em hold em when he is on a flush draw that isn't runner-runner. In those situations I know that he wont make it 65-66% of the time. So, I usually make it outrageously expensive for him to stay in it. I've bet three times the pot before and gotten him to call. When I win in a showdown it is great but I have seen him land it at least twice.
But, typically, if I put my opponent on a flush or straight draw, I try to give them the wrong odds to chase it. The nice thing is that if they need the one card and they miss on the turn, you have another chance to give them the wrong odds and win the pot without a showdown.
And, I would rather overbet in that situation because at least I know they are not getting the right odds to chase it, and the 'correct' move for them is to fold. If you underbet, you are giving them the right pot odds
to chase it and it can back fire on you.