No, not a design flaw at all.
If the supercharger isn't working properly (clutch has failed) and not creating boost then the total power output will be down significantly. If the impeller and pump selection was setup for say 250hp, and you're only making 190hp, then you can't push the prop any faster. Underpowered boats (by design or by malfunction) exhibit the symptoms of being unable to reach full revs, and being unable to attain decent speed. When compared to a similar boat that is running properly.
The symptoms point to a significant loss of power since we know that engine/prop/pump combination works well together in other similar hulls......Also, the power loss is more than just dirty plugs or clogged air filter. Would have to be something major, and these engines are known for failed compressor clutches. So, that's my guess.