Well, Dukat died after Winn poisoned him as a sacrifice,(lets dwell upon the irony of the Traitor being betrayed) and the Pah-Wraith's used the corpse as a host for the Kosst Amojan.
So Dukat was long dead by the time Sisko realized that the Fire Caves had been opened. What remained was merely a vessel and was burned in the fire. (although the scenario that JK
outlined could have been the case, in which case in a thousand years...
As for the Cardassians I would imagine that Dukat would be tried in absenta
for treason and would be marked for death (along with Gul Revok, the Founder and each and every Weyoun clone). Poor old Macet would have a really difficult few years of course.
I guess everyone else will assume that Dukat is in hiding waiting to return. Perhaps he will become an evil legend on Bajor?