I don't think a flooded Ecumenopoli makes sense, but a flooded relic world sounds interesting.
Let's say you use a Deluge Machine on an Ecumenopolis. Right now it becomes an Ocean World? What if it turned into a Flooded Relic World, instead? Increase the size of the planet by 50% to account for all the water it would take to flood the arcologies (and also not feel bad about losing the ability to build them), add the standard Relic World features (including blockers), and make the planet non-terraformable -- not into an Ecumenopolis, not into a Gaia World, not into a Tomb World, it can only be turned into an uninhabitable world. Habitability is as a Relic World, except Aquatic gives a bonus on it instead of a penalty, and it also counts as an Ocean planet for Anglers.