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Roots are inefficient - they are blowers where centrifigals and screw (i.e. whipple) are compressors. The inefficiency equates to heat. Since you have an unlimited amount of cold water available, air to water intercooling the inlet charge addresses this nicely.
For large cubic inch applications which are not running at seriously high RPM, a Whipple is better suited than a centrfigal. Centrifigals are better suited for very high RPM applications.
For a typical boat, large cubic inch engine with redline under 6,000 RPM, I would say the Whipple is th best choice for the application.
However, a turbo would be even better as there is less sacrificial loss of horsepower - no belt to drive it. You can run less bost and make same HP levels. I am not sure about the whipple, but a centrifigal can easily eat up 80 HP just to run it. So to make X horsepower you need to run more boost than with a turbo.
Turbo's are more complicated setups and generally cost more. Not sure why there aren't more turbo's for boats as they are better solution for forced induction applications. Would be harder to have standardized kits as packaging would quite different for different boats. Superchargers allow more standardization and this makes it cheaper. If I were building an all out effort (i.e. custom, cost is no object), I would be doing a turbo setup.
John
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