What will blocked water box do to jet ski?

A blocked water box will prevent water from flowing into the exhaust system. Because jet skis have a fully-enclosed engine space, cooling of the exhaust system is vital to prevent overheating. With no cooling water flowing into the exhaust system, the exhaust system will overheat.

Exactly what happens depends on the model and to some extent on luck. But usually one of the exhaust connections will burn through, causing exhaust to leak into the bilge.