The objection in TFA was ecological damage due to de-oxygenation of the water. They don't mention boats as a problem so I'd guess that's taken care of?

As for the size of the laguna, they're talking about walling the whole thing off so some circulation pumps shouldn't be too much of a stretch. Alternately they could install some kind of bubbler system (like a giant version of a fish tank air pump) to keep the water aerated in situ. Again, it's not going to be pocket change but it's an option.