I know some F115's had issues with water getting past the bad lower oil seals. The early F200, 225, and 250's I think all had various issues with the lower oil seals (under the oil pump) but more normally an oil leak issue rather than water ingress on those engines I think. If you drop the lower unit and find engine oil on the top of the drive shaft you probably have the oil seal issue. Fix usually involves a Speedy Sleeve as well as a new seal. Of course the other well known issue on many of these gen 1 F series Yamahas is the rotting exhausts. That might explain the noise difference and maybe even the water although I haven't heard of water in oil being a typical symptom.
