Yes water temp will affect Tuning Some, BUT engine temp is greatly controlled by Air\Fuel Mixture. a Rich Needle will run Cooler and a Leaner Needle will run Hotter. Engine temp is how you tell when you're getting to the right Air\Fuel Mixture (needle setting).

As far as Water inside the hull,, Some water is Normal it will Splash in Any and All Cracks and Crannies around the cowling Especially if you're running it Hard.