The problem with the ship submerging for the fortify is it would have to go back down again during the last attack in order to flow with it rising up in the beginning of the first attack, which would look weird and quickly get annoying with the ship constantly going down and coming back up again during a battle. I'm thinking the animations are going to go something like this:
Default: Sitting there as usual
Run: Normal above water run
Fidget: Submerge and rise up (so that animation will be rather lengthy, but fidget only happens once in a while so it won't look weird when it happens)
Fortify: Bow cannon ports open and bow cannons pop out (even though they won't be used in the standard attacks, still looks like the ship is getting ready to fight)
Attack A: Broadside
Attack B: Kraken hammer rises, comes down
Attack C: Kraken Tentacles whip around
*other attack options, you'll have to change the ini file if you want these, suggest you don't mix them with the default attacks*
Attack D: Bow cannons (facing towards enemy)
Attack E: Kraken Hammer (facing towards enemy)
Attack F: Kraken Tentacles (ditto)
Victory: Not much animation, but the sound will be a clip of Davy Jones playing his theme on the organ
Death: Sinks, to show that it really is dead and not just submerging there will be some masts coming down too