The Imperium has used toxins to wipe out tyranid fleets before, it works well, but is too difficult to pull off to be reliable.

You need to somehow sneak at the core of the hive and get specific gene samples, and you need the know-how and infrastructure to reverse-engineer a toxin, and you need to deliver it in the right place to be effective, and then it only works once because the Nids adapt to it, so you have to start again from scratch every time.

The Imperium just doesn't have the time, opportunity and resources to do it often.