Heh... no nano rippers?
Dude! You gotta get that fixed!
Dunno what the problem might be. I've never had any difficulty.
To see if it's possible to use mass driver weapons, or if your game is somehow crippled, start a new game. The first screen is Galaxy Setup. In the upper right, chose Scenario 'Battle of the Gods'. Then continue to start the game normally. This gives you all techs from the start.
Then get to the ship builder. Create a 'new' ship, select a hull and then select weapons. There are three choices under the weapons tab, Beam, Mass Driver and Missile. Select Mass Driver and you should see things like Black Hole Gun, Neutrino Bullets, Spike Driver, etc. Scroll down and you would see Miniballs, and Nano Ripper etc.
The game is stored in two places. First I'd try to Uninstall via the control panel. Uninstall both Stardock Central and Galactic Civilizations. Then go to c:\Program Files and delete the Stardock folder.
The other part of the game is stored under My Documents\My Games\Galciv2
I'd delete that whole folder too.
Then re-download the game and re-install.
I dunno. Good luck though!