Hi,
adding custom textures (or making them more transparent) for the ores which spawn "under"water would be really nice, because currently they are just slapped on top of the water surface which looks weird.

I like the idea of ressources spawning in water, it integrates pretty well into the gameplay in combination with cargo ships

Unfortunately not something the engine really allows. The sprites are set for each resource and the only changes they have are just how many resources are there. Only way to change their look is to make a completely new entity with the new graphics and swap the new one in when the chunk is created, which is a lot of work and easily breakable.

Base game and other mods have similar issues, like with grass and such not being able to appear over the ores when it spawns on tiles with long grass. The way the layering in the game works means the tile sprites can't ever show on top of a resource.