[King Yao]

I think you have a good point. With one flush card in your hand and two on the board, I wouldn't bother to count any flush outs at all. The number of outs are the same in the two situations, but the other players will play the hand, and react to your hand differently. You could reduce the expected pot size, but for me, it would be easier not to count the flush outs at all.

With two flush cards in your hand, if you do hit the flush on the River, it will be hidden and a surprise. You are more likely to be paid off. On the other hand, with four flush on the board, you are less likely to be paid off, and also more likely to be trumped by a higher flush.