Hey, the original draft had the multiplier as x10.

The reason I gave the ships the multiplier is because I didn't want ship-to-ship battles to end too quickly. Spaceships in RJ are huge, massive machines, and ship-to-ship battles should be important events, not something you want to gloss over or speed through.
Despite the obvious Star Wars/Trek influences in the book, the spaceship rules were more heavily influenced by a computer game I used to play a lot called "Space Empires" and the Buck Rogers video games. In these games, you pound and pound on enemy ships with heavy guns, even after the shields are gone. Systems degrade and your crew races around trying to decide what systems to repair.
So it's a taste thing, really.
If you want to drop the modifier for your games, I certainly don't have the resources to hunt you down and stop you. I can certainly see dropping the modifier for "nameless mook" ships.
(As an aside, getting rid of the multiplier as you did in the Sex, Lies, Ultraspies car rules makes perfect sense, thematically)