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I doubt the heave and ho of the ocean would affect spinning disks like hard drives. We used to put hard drives in iPods that got thrown around by people jogging with few failures.

What is a concern is salt water, wind blowing the surface of of the ocean can add salt into the air that will eventually get into the containers. Salt moisture will be a huge long term problem.

The salt issue is something that's probably already been solved (couldn't find any information on it though). There are underwater science labs, medical rooms at sea, and probably tons of research into how to keep salt out of computers from the US Navy.

For a boat that big you're never going to get accelerations higher than a half G or so, and water is squishy so the jerk is going to be very moderate. I expect that frequent acceleration will actually have some impact on how fast the hard drives wear out, but not a large one.

Protecting everything from salt spray is going to be the bigger concern.

This would be far from the first time electronics were put on a boat.