Don't forget to count outs at their true value ... for example, your baby flush draw is somewhere betwen 7 and 8 outs, not 9 like a nut flush draw.
...???... An out is an out. If you feel some of the cards that will make your hand will still leave you with second best then you simply don't consider them to begin with you (ie. a flush card that pairs the board). If you have a draw like a baby flush and you think that someone might have a higher flush draw your number of outs is zero. If you don't feel the cards you are drawing for will give you the best hand then you simply don't draw to them.