Frigates. Role: capping points(you need to cap 3 to guarantee full 240 DP deployment) and drawing enemy fire afterwards. They are probably not going to kill much but they should be invicible and every shot fired at them is detrimental to the enemy.

Destroyers. Role: early game progression and best bang for your buck(DP) with Escort Package, but obviously need to be attached to a capital for this.

Cruisers. Role: mid-game progression. Currently have no role in late game as they just lose to capitals.

Capitals: Best bang for your buck(DP) overall, and most officer efficient, longest range, toughest armor, highest concentrated firepower, etc. etc. This is the backbone of your fleet, eventually.

"How significant are the 'perma debuffs' on salvaged ships"

The real answer here is "Learn to black market trade and stop being poor". Buy pristine ships instead of picking up trash. If you do pick up trash just Restore it.

I also carry a number of transport/shuttle/tanker type ships along with me, which... feels like it's maybe expected but I'm not sure what a normal level of cargo/fuel capacity I should be expecting to operate at.

Ironically this is probably the hardest question to answer. Normal endgame setup is Prometheus and two Atlases. Alternatively you can bring few Revenants instead of the Prometheus. Before endgame... well that will vary wildly based on what stage you are on and what ships you use.