I had one in my Seadoo 951 based on recommendations by Bill O'neil and Harry Klem. Some skis are notorious for creating bubbles and super sensitive to their ingestion and that ski was one of the worst for both. There was an army of tiny bubbles marching down the fuel lines at all times. Tuning was night and day after installing the separator.
The Yamaha's however are not really known for having that issue though, not in near stock form anyway. It really wouldn't hurt to add one to any ski but I really don't think it's your issue.
Is the idle set really low causing a ton of vibration? That in itself can cause fuel aeration.
Otherwise, I'd recommend you broaden your scope a little and give a few other items a quick once over. Have you tried fresh plugs? Close up the gap? You mentioned water ingestion, have you checked compression after? Was there enough water in the hull to reach the ebox? What shape are your coil wires in? Are you running a coupler cover?