Sure. Early landing capsules were designed to land in water. Shapeships need to be airtight, and any craft capable to blasting through the atmosphere ought to be able to handle water pressure. Some might suffer if/when they get really deep underwater – not sure about that.

I’m no NASA employee but I would think that blasting off into space at mock-something speed, circling the moon, and reentry into the Earth’s atmosphere at extreme speed and temperatures along with splashing down into the ocean. should qualify.

If you define positive pressure as pressure trying to get into the spacecraft and negative pressure as pressure trying to get out of the spacecraft, all modern crewed spacecraft are designed for at least 14.7 psi negative pressure (since that’s what is nice for astronauts to breathe). The ones that land in water – Crew Dragon, Orion are designed for some positive pressure because they might go underwater a short depth upon landing. But air/water pressure would be evenly distributed, so that’s easy to design for. There are big mechanical loads from the launch and from the landing impact that come at specific directions. Those are harder to design for. Just have to make their best guesses and design for extra.