Midtin,
The main reason it is most often mounted on the right side is because of transducer cable length. In most boats, the console is on the right side, so easier to run cable, shorter distance, etc.
So, either side should be fine, if the cable is long enough.
The one thing I try to stress is getting the GPS reciever as close to the transducer as possible. This will give you more accurate waypoints when marking structure, etc.
Hope that helps.
Robert