What is the likelihood of water coming in the side scuppers when drifting or anchored and wind pushes you broadside to the waves? Would the flaps stop the waves from pushing water in?

Thanks for the info. I'll proceed with the side scupps.

I have NO experience with side scuppers, but, I wonder why majority of open fisherman type boats don't have them? What are you trying to accomplish by self bailing out the side vs the transom? I would be concerned that if you did not have deck gutters that drained to the suppers that you would run the risk of water ponding against the fantail. I would reconsider your layout.
Just my 2 cents.

Sorry guys, I've been busy with getting the new shop going.

Absolutely YES. There is no way I would go back to transom scuppers. I will get a pic tonight of the final set up that has proven to work in the worst conditions. I can't believe how fast they clear the deck of water an fish parts.

I will also advise against the flaps as they hinder the free flow of water out. A shield is far superior as long as you have your decks high enough.

If you get a chance a pic would be great.

Sorry, I promise to get you some pics.

Found some. The clam shell covers the front third as a deflector.

Thanks for the pics. I may start with the clam shells and keep the rubber flappers incase I want more protection.

Side vs Rear Scuppers
 

I am Liking the idea of the side scuppers but I have a few questions/concerns about how they are set up. Are you still using the the original deck drains with a 90 degree elbow out to the side? I won't be using the liner but would it be better to use a floor drain with a tube to the hull or just have the scupper drain directly from the deck?

Straight off the deck. No plumbing. Like Kmoose said, even fish parts go out.