there is a way buy i dont know what it is. i think it has to be buffed with a diamond polishing wheel. they look just like a grinding wheel but there for polishing stone. they use them for solid surface polishing on counter tops.
Yes, you can buff out minor scratches with a glass buffer, but it takes alot of elbow grease and the scratches need to be small. You should be able to pick up some buffing powder from most glass companies. I have done it before on a window. It probably wouldn't be worth doing it on a fish tank though. My guess is that scratches that you notice when water is in the tank is too deep to be buffed out. The buffing itself can also distort the view through the glass.