Nicks in the bottom may be ok if they are small. Nicks on the side of the transducer may affect the SI a little. If they can trap air bubbles, then you will surely have problems. If you do sand them, make sure you finish with a very fine paper.
The SI elements are on the outside edge looking down at 30 degrees. Here is a diagram. As long as you dont have any nicks in the blue area, you will probably be fine.
Good Luck,
Robert