Correct me if I’m wrong, but i think MFM doesn’t change anything on warships.
It’s only making changes on Merchants as the title says (Merchant Fleet Mod), and i don’t recall seeing any warship in MFM sea folder...
Of course there is a way to reduce the ships wake Wave height, you’ll need to open the ship.dat with S3D and find the Wake wave node to lower it. Or maybe in the ship.Val you’ll find wake wave values...