What are these?
 

Down by the drain plug? Guessing high speed water pickups for a genset????

I'm guessing they are supply lines for the engines. The only way to know is to see where the lines run to inside.
I had them on my 29 for the intercooler supply lines.

Yep. Water Pickups. Though a genset wouldn't need two of them. Most likely they're for the engines.

Some kind of aftermarket extra water supply to the engines in addition to the drive pickups?

My genset's pickup is in the bottom of the hull. Thought it may be so gen can be run at speed.

Engine water pick ups for sure. My drive pick ups are capped off. I could never get enough water thru them to keep the engines cool. +1 on why would a gen set need 2 pick ups. My guess is their plumbed into the strainer in ports?