$2/$5 NL live.

I limp with [9h] on the button after 2 other limpers.

Pot $25. Flop [Qd][Jd]. Blinds check. A limper bets $25. A fold and then I make it $100. Folds back to him and he shoves. Its $400 to me. Call or fold?

I think it's WAY more likely that he just has the A[d] or maybe a set than the small flush.

How many people live flop a flush and lead FULL pot with it?

I think in a live game, barring a read, this is a standard call. too many people are shoving x, or something weird like KQ here for you to be worried about AT or a flopped flush.

There are very few hands the crush you, and the range of hands that beats you is smaller than the range of hands i think you can beat here.

In the end, i think calling the push is +EV, though i think it may be only somewhat so. However, since you already have $100 invested in the pot, i think the argument for calling becomes stronger