Two seals?

The Wind Waker says that the Sages' seal has failed and Ganon is obviously
free to roam the world once more, but his monsters are still frozen by the seal
of the Master Sword... what exactly does this mean?

Well the first seal you were talking about was just the general imprisonment seal put on at the end of the adult timeline of OoT. That seal got broken.

The second seal is basically the Great Flood, which was put on AFTER Ganon escaped and broke the first seal.

My bad, I forgot that the Sages' seal was broken before the MS seal was put in place