The most difficult aspect with a boat tunnel is the way how the boat graphics are handled - forget vanilla boats, how'd you make it work (or not work) nicely with FISH2 or Sailing Ships NewGRF ?
Eh... boats already look rough when they overlap each other. I'm in favour of just adding a tunnel and letting players use it or not, as they choose. NUTS already has the graphics under a creative commons licence.
What I'd really like is a way for WETrails (part of NUTS) to be laid on the ocean, but that's another issue.