So are the words for Autumn and October the same? And if so isn't this confusing without Mis before?
People will use mis Hydref if it is not clear from the context that they mean the month rather than the season. It is not a problem in practice.
The same thing can happen with dydd Mawrth, mis Mawrth, Mawrth (Tuesday, March, Mars) - the context usually makes it clear which Mawrth is meant.
(Edited to correct day of the week)