1. Whenever possible, you want to keep the same energy type and stick with either beams or cannon/turrets and either mines or torpedoes. This way you can more effectively boost with your tactical abilities.
2. It's more than reasonable, and most of the time what people do, to have one set of items that you use on every ship. I would probably end up setting both ships with the best gear you can find between the two ship
when the Na'kuhl use their plasma wave, just move out of it