Modern VG turbos are extremely durable and are meant to be constantly cycled. The newest engines use the VG to help control emissions, with a side benefit of performance. All 3 major pickup truck diesels are using VG now. It is well proven and durable. Really, VG is a potential solution, with one caution, related to your point about car vs boat.
The VG doesn't really react all that fast. The control system is seemingly well damped to avoid "overshoot" and thus overboost when moving the vanes. You really don't want to overspeed a compressor wheel! As such, it may not be ideal for a situation where the dynamics are changing the way they do in an offshore type environment. The only way to know for sure is to try it.
Generally, marine duty cycle is thought of as more steady state than on-highway. In the case of an aggressively driven offshore boat, it may very well be the opposite. Compromises will be made when the needs of one group of customers is drastically different from another. So, with VG, where you have an extremely dynamic environment, if could be excessively difficult to design a control strategy that fits multiple uses (which it must due the the financial constraints). What would you reference the vanes position to? Boost, TPS, RPM, turbo speed, etc. The interrelationships here are not trivial to establish, and it's never going to be optimized for anything but one specific set of conditions.
This is traditionally true, but there are things that can be done here that would surprise you. With a late post injection, fuel can be delivered to the cylinder at a point where it would contribute little or nothing to the torque output, but put a lot of heat into the exhaust stream, driving the turbocharger to maintain boost. It would likely be less extreme than the "launch control" or "anti-lag" used by boosted race cars where gasoline in injected such that it ignites in the exhaust manifold, pre-turbo, and very aggressively, to build boost without actually loading the engine. This system will destroy a turbo in a hurry. http://youtube.com/watch?v=gOnYA3N46kk&feature=relatedA diesel boat can't really stay in the power band when the props leave the water, the governor forces it to idle mode???
Use of this type of strategy in a diesel will happen someday, though I'm not aware of anyone doing it today. Development is ongoing with electrically assisted turbos which could have a similar effect. When the exhaust gas energy falls, the electric drive takes over to keep the shaft speed, and thus boost, up. This may be a couple of years out for any real production applications, and you won't see it in marine for sometime after that.
Like I've said, we've only begun to explore the performance potential of this technology...and we have the environmental people to thank for forcing this development with air quality regulations. Most diesel innovation today is focused on reduced emissions. Re-applying it for performance reasons is a side benefit.