So, if I use Flamer Attack and Zael rolls a 3, but the swarm only contains 2 genestealers, does that mean that he kills no one because he can only kill the exact number he rolls, in this case 3? That's how I played it and if so, it's of very little use if you are working hard to keep those genestealer swarms small.

You kill that many GS, or as many as the swarm has if it has fewer.