You can modify quite a lot of the game, including the ship stats and their equipment. This guide looks like it should be able to provide a lot of help.
I personally have not modified the game itself, but looked at the Stardock forums to get an idea of what things a person can change. Modifying the game looks like it is fairly easy to do. It's something I'm thinking of doing eventually. Here is a link to the Stardock forums:
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