I think that I might be loosing a lot of value because I am betting too big when two suited cards come on the flop.

Let's say that I am on the flop against a very bad player:
I have AK
Flop is K72
VeryBadPlayer checks. At this point I know that he has no made hand, and he is so bad that whatever he has he will call a small bet and fold to a bigger one.
In such a situation, I bet big to protect my hand from a spade flush draw. So VeryBadPlayer folds.

I wonder if I should bet small for value instead, as (if I am doing the math correctly) there is only approximately 5% chances that he has two spades.

What do you think ? Is it a problem to be too scared of flush draws?

Thanks for any advice!

There is no reason that your value bets can't deny them proper odds. In micro limits most people do not understand pot odds and will call down any amount with a draw. Just value bet them to death.

2/3 pot is good so that you can deny him explicit odds for flush + value

You want to consider both suitedness and connectedness when examining board texture. A 'wet' flop will have both. A Ks7s2d flop is actually relatively dry even though there is a flush draw out. Vary your bet based on your villain, but ~ 2/3rds psb should be fine as a default for a flop like that. It is when you have AK on KsTs9d that you want to bet near or full pot because so much of a players range will hit that flop with flush draws, straight draws and made hands (pair+).

Generally speaking, betting between 3/4 and the full pot here will get you adequate protection and lots of value from a calling-station like this.

You should really be more worried about the value end of this equilibrium than the protection end. A calling station like you described will call down with really lousy draws. Your main job is to give them improper odds to do so. Fortunately it's not too difficult to play against these types of players - they play draws and middle pair the same way, so just bet bet bet, get your value, and slow down if a scare card comes and they wake up suddenly. Calling stations usually let you know as soon as they pick up a hand so as long as you're capable of putting on the brakes when played back at they shouldn't ever give you trouble.