Geodes whose cavities intsersect liquids do not get flooded. This seems unintentional since they are geologic features like caves and therefore canonically existed before the world's liquids settled.
Version: 23w46a
Seed: -9032499138528639197
Coordinates: /execute in minecraft:overworld run tp @s 11966.7 19.1 12125.7 -959.5 33.5
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Amethyst geodes generating on the ocean floor is intentional, however, them not being waterlogged would be considered a feature request therefore making this report invalid.

I've seen waterlogged geodes before. In this case it was exposed to water in an ocean but wasn't waterlogged, therefore it's a bug.
Hi! After some research, I've found that it's impossible for amethyst geodes to spawn waterlogged, therefore making this report invalid. Water is able to flow into them, but they are unable to spawn waterlogged. 🙂

It was decided on the Mojira Discord to reopen this for a Mojang employee to decide.