Thanks for the reply, Mularac!
In regards to the damage capacity of ships in my mod, suffice to say that it will be generally unreasonable to expect to finish a mission with all your ships intact - especially against the default skirmisher AI, which focuses all its firepower on a single target. There are exceptions, of course - if your only ship is a Fleet Carrier, the strongest in the mod thanks to its Level 2 Screens (reduce incoming damage by 66%), 980 HP, two medium range beam batteries, and six wings of fighters, and your opponents are all Courier class vessels, with no anti-fighter defenses, 20HP, and only a single short range weapon of their own, then odds are you'd have to play really poorly to see your Fleet Carrier be taken down. Most scenarios, however, will see you fighting against an equal or greater number of opposing ships with around the same degree of fire power as your own.
As an example, the scenario I just finished creating pits you against seven enemy vessels (in order of increasing potency, two destroyers, two light cruisers, two escort cruisers, and one heavy cruiser) while granting you five expendable combat vessels (three heavy cruisers and two needle cruisers - specialized ships using the heavy cruiser chassis, equipped with level 2 screens and armed solely with anti-device weaponry) and one unarmed but highly agile drone that you must escort to a nav point on the far side of the map. Selecting the drone allows you to summon reinforcement ships - needle cruisers or heavy cruisers, both of which take 30 seconds to arrive. Though it is possible to complete the scenario while losing only a single ship, I've played the mission at least two dozen times over yesterday and today and found that it's more likely that two or three casualties will occur, despite the technically superior armament the player is given.