Could Water get into the exhaust pipes?
 

I've always wondered (worried) about being stopped in rougher water and having waves come over the swim platform and thru hull exhaust pipes. People standing on the swim platform can also lower the exhaust pipes to water level.

How does water not enter the engine? Or how bad can the transom be hit with waves before this is an issue?

Thanks!

That's what exhaust flappers, or valves prevent.