They did do that, back in the mini-series. They got out of that one by reverting back to an older software suite. One that wasn't as complex and less networked. Hence, they have to dumbfire the missiles.
They can always try to fabricate new missiles. They constructed a fighter, why not missiles?
If we put this all together, it sounds logical. Missiles may be better at long range, but if the enemy can jam the guidence, then that makes them combat ineffective. If they are dumbfired, then the enemy fighters can just avoid them, at long range. This would apply to the Vipers. Vipers would also have to fire them blind. They can't waste missiles like they do with their bullets since missiles are a bit more costly, resource-wise. And if the enemy can jam them, what's the point of wasting missiles on small targets when they could be saved for the big ones.