Don't know what to tell you, man. You sound very confident, but I literally have a bachelor’s degree in Maritime Transportation and Navigation, and have served on several cargo vessels, as well as a couple of passenger ferries. I might have exaggerated with 90%, I'll give you that, so take it down to 80%.

cruise ships are 10% underwater

As I said, those are usually mostly above water, to prioritize comfort. But even those are at least 30% underwater, with very low center of gravity. You can't have a ship 90% above water; it would keel over. Except some heavyweight barges that have big surface area, I suppose.

A fully loaded cargo ship can’t be more than 30%

In fact, that's about the least an empty cargo ship is underwater. Because when empty, cargo ships take ballast to prevent capsizing. Also the propeller is designed to be at least a few meters below water to be effective.

they tend to be stacked far higher than the ship’s sides

I think you're focused specifically on container vessels. Those still have way more massive holds than the containers you see on deck.

Ocean waves would easily swamp a ship that was 80-90% underwater

Depending on the season and projected weather conditions, ships are leaded to a different extents. They have load lines for winter and summer. In summer, for certain cargo ships, the freeboard can sometimes be measured in centiliters. I remember being able to kneel on deck and reach the water with my hand. In heavy seas, the waves are constantly on the deck and the ship can handle it fine; you just don't go there.

Ships often look deceptive about their draft, because you almost never see a ship truly empty. Even when not carrying load, they have a lot of ballast.