There was a minor reference to FF Mystic Quest during ARR - a side quest in Coerthas Central Highlands had you searching for a stray black sheep named Benjamin, which is a not-very subtle light-hearted stab at FFMQ's 'black sheep' status in the FF series - Benjamin was of course the name of FFMQ's main character.

Whether you would see any further references is anyone's guess - SE seem to be adding the in-jokes and references to the rest of the series including spin-offs more and more, so more FFMQ references are possible presumedly.