Once PDC is available, missiles are generally useless. They can be good as a surprise attack against an enemy that neglects sufficient PDC, thinking that they don't need it. But after that, you had better have beam ships to handle their next fleet.
You can of course try to overwhelm enemy PDC with fighters, missiles, and drones. This takes a huge amount of micromanagement and a lot of resources anyways, so you are probably better off just sticking with beam ships...