Definitely save a template without any equipment. What I do is create a template, save it. Then load the template and equip. Each time I upgrade to a more powerful weapon or drive I change the number. Something like Little Wing B1 for my first ship with a beam weapon. M1 for missles, P1 for projectiles(cannons). Though I do not use projectile weapons since they're so awful. When I upgrade the drive or weapon it becomes B2, B3, and so on. When I start a new game and am using the same ship set(Dregin, Iconian, etc) I often have to delete the ship designs from previous games because they the capacity goes over the limit or too far under it when I'm ready to build a new ship.

Cargo ships have a lot less hitpoints than other ships. They're for colonizing, trading, and constructing. As for increasing size you can enlarge parts from any size set using the ship editor. Most ships appear small on the map, not sure how big you'd want them to be.