I think Bruce summed it up very well. If you want/need/like single engine economy, lighter weight, and better engine access, buy a single engine boat.
If you want/need/like twin engine maneuverability and redundancy, or like me simply like operating multiple engines-- I love hearing the big whale watch boat in our marina fire up; it has three engingines-- then buy a twin engine boat.
But to my way of thinking, buying a twin and then trying to operate it as a single is a waste of time. Even if a prop can be freewheeled without damaging other drive components, you're not saving anywhere near enough fuel to make up for the higher purchase price, higher service, maintenance and repair costs over time, reduced engine access, and doubled weight the boat has to lug around and that the one operating engine has to push.
I believe in the overall scheme of things running a twin on one is a false economy. The few people I know who do it, after hearing their reasons why, it's obvious to me that they should have bought a single engine boat in the first place. It would have served them much better.