I always shut all but one down.
Around Ft. Myers we have a number of slow zones.
One of the boats I sold had 50 hrs on it. When I pulled up the log on the Smartcraft, 27 hrs were between 500 and 1500 RPM.
Beside cutting down the hours there have been studies that show you do burn less fuel by running on one engine.
If you look at all of that it seems like there's no good reason to run more than one.
Of course if you have power steering on just one motor it gets a little trickier.