Hmmm, this is a bug that seems to happen when you upgrade your old ships with new weapons and what not but keep the same name. As long as you don't save/load the game you'll be fine, but when you do all the ships appear.
I think it was fixed in the latest patch - did you get it?
If not, the easiest fix is 2-fold
1- Rename your ships with a "Mk2" or something at the end of the name when you upgrade them
2- go to your my documters/my games/galciv2/ships folder and find and delete all the duplicate .shipclass and .shipcfg files that bear the same name but with a different number. (for example, scout0.shipclass, scout1.shipclass, scout2.shipclass)
Step 2 will get you rid of the clutter, step 1 will make sure it doesn't happen again