Maybe they don't use the evil flesh eating virus on nids because they're afraid of them 1) building up an immunity - or more horrible: 2) they manage to adapt it into their own DNA and now every Nid is now a carrier.
actually there is one piece of background in one of the BFG books / Magazines (I think it was in Armada, but not sure), where the IN tries exactly that: virusbombing the Nid ships, only to see that it has limited effect and the Nid boardingparty's 'poisoned' weapons actually has the same/similar effect as the original virus itself.
edit:
ahh found the quote from the book, it was in Armada:
"a fatal error, 'twas, listening to that damned old fool. We were carrying virus bombs for the planet below, but hergol told us since we were in a jam, we might launch a few at the things in space, only it didn't do a thing to 'em.
Well, so we thought until the damned things rammed us a week later and got hold of the ship. They spat this acid, this burning spittle everywhere, and within and hour, those that
didn't die from the burns were sick as hell with the same virus we'd hurled at the beast to begin with."