One of the ways that was planned to mine undersea coal was in situ gasification: basically, start a Centralia-like fire, pump down oxygen and steam, and recover the mixture of carbon monoxide and hydrogen for use as a fuel. If it's undersea then the risk of uncontrolled introduction of air (as occurs at Centralia) is reduced.
The famous Hashima island (also called "Battleship island") in Japan near Nagasaki was an undersea coal mine - the network of tunnels even connected to another mining island nearby.
I don't think they ever had problems with flooding from the sea, but it was certainly dangerous enough to work there due to regular mining and industrial hazards. Also apparently it was very hot and humid in the mine.
The claim on Wikipedia seems to be they have not done so to the satisfaction of the other unesco members who had to vote for its inclusion as a heritage site.