Yes, over the course of time more and more inactive AI characters and ships build up in the database - you'll see your saved games getting larger and larger. This has the effect of making things move ever slower.
The online servers (EAW at least) get around this by running a "cleaner" program that weeds out all these dead and useless beasties, but that hasn't been available for SP (or OP) so far.
I'm currently in the final development stages of an editor/cleaner that works for all four flavours (OP/EAW, single player & server) but it's still got some glitches - I would imagine it's 2-3 weeks away from a beta release. Once it's ready it will allow you to clean the deadwood out of your game, and also to edit your saved games (change your prestige, race, ships, alliances, mission lists, etc etc)
The file you want to edit to change the starting prestige is:
MetaAssets\ServerProfiles\Singleplayer\Character.gf
You'll see a setting in there that looks like:
//This is a character's starting prestige
StartingPrestige = 100
change that beastie to whatever value you want
dave