I'm not experienced with Ontario, and I would encourage you to consult with the Ontario Project which is a subproject of the Canadian History Project. That said, it would seem to me that these villages would be similar to the villages and towns in the United States that were submerged when the Corp of Engineers or other government agencies built dams for hydro electric power or flood control creating many large lakes. And those in turn are similar to places which became ghost towns for other reasons such as the mechanization of farming or the flight from the dust bowl in the 1930's. The big difference with former towns that are now submerged is that there is usually a specific date or small time period when the submerged towns became extinct and there usually is not one for ghost towns that gradually were abandoned. They are all types of historical place names.
There are several different ways of handling historical place names which have been discussed in prior posts. Check out this G2G thread.
My personal preference would be to put a date qualifier in the category name to alert users to the historical nature of the place name and an explanation on the category page something like the following:
Mille Roches, Ontario, Canada (before 1958)
with an explanation on the category page describing the submergence of the village by the Saint Lawrence Seaway Project in 1958. However, most of the ghost towns I've found in categories on Wikitree do not use the date qualifiers and many do not even have descriptive information on the category page indicating the community no longer exists.
