I just turn up the game speed when lulls like that break out (because of them moving slow), but you technically can mod the ship speed to make them faster.

Are you playing with the Fast/Faster speed settings for all speeds?  That would help.  Sins isn't like a traditional RTS; it's slower, but it's awesome once you get into it.  I think you can use the + or - keys to adjust the speed if you are playing single player.  (Note that it has an online multiplayer component for after you've learned the game.  It's awesome to play it against other people in 5v5, though most of that activity is for the Diplomacy expansion.)