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Ecumenopoli still get turned into Ocean Worlds. Just because there's a city there doesn't mean it cant be filled with water. Maybe there can be a special modifier for the planet that signifies there's a sunken city-world there.
Habitats get destroyed. Filling something with water tends to break it, and I'm sure all that water pressure will create a leak or two.
Ian M Banks actually has an Ocean ringworld / habitat (the term he uses is 'orbital' and I forget the exact scale) in Concider Philebas. One endless loop of ocean confined my dams at the edges, with only scatterd islands and vast urbanised barges as solid features. So water-ringworlds have president in the genre.