I've been torn on this one, and the same with NPC's in general. Although I find myself swearing to myself when NPC's are in the way, like GB's with CD's...I remind myself that not everyone is a vet, and there has to be some base level of challenge, especially for newcomers.
Having said that, I think its better to put CD's back on VHF's, not gunboats...why? Because you can kill NPC fighters much faster and easier than gunboats, especially when you're in a transport. It may slow you down as often but you could get rid of the ships with CD's faster and get moving past the GB's, instead of the whacky stuff you have to do to avoid being roasted by a swarm of CD gunboats you have no chance of eliminating in most transports.