It's because Escort ships receive a shield HP penalty.
For example if you get Paratrinic shields they offer 7500Hp on a Science ship, if you put them on a Saber you get closer to 4500 I think might be a bit less.
It's to compensate for all the DPS you can do and tbh that's fair enough, Escorts are literally like fighter bombers in this game you can't take a beating at all but you can do some serious damage, you gotta work really hard to stay alive well you did prepatch lol
Yes it seems like Science gets a 1000 point boost and escorts get a 1000 point handicap. Cruisers seem to get a small handicap not much though.