Whales blocking ships is always annoying, in particular in battles when one has to retreat, even more because they are moving and changing directions.
The only argument to not have them blocking has been that the models would overlap, which would look unrealistic as neither of both are ghosts.
However (1) the corpse does not have the blocking property but the same model and position and (2) it doesn't look that bad if you check the gifs and (3) it is not unrealistic that whales swim below ships.

Worst case mentioned by Sandarac should be this jumping animation on sicilia nomad, but it is hard to trigger since the period of overlap is very short as the whale always moves, the ship too mostly:

Other worst case mentioned by bb:

Notice with the front and rear end of the ship, collisions already occur:

See the patch in action on cycladic archipelago and try to produce the worst case scenario.

Notice that both properties are needed:
<element name='BlockMovement' a:help='Whether units should be allowed to walk through this entity
<element name='BlockPathfinding' a:help='Whether the long-distance pathfinder should avoid paths through this entity. This should only be set for large stationary obstructions'>"

Persuade yourself that those are all templates by searching for "<PassabilityClass>ship"