That would then imply that they've been destroyed.
Yes, it is most likely that they are no longer around. But, if they are still around, they would no longer be in Vvardenfell.
To clarify, it was the nords of Solstheim, NOT Skyrim, that gave lots of charity to the dunmer in MK's hint. In Skyrim, I would gander to say it was a lot of refugees living in the good graces of the nords. Having the Camonna Tong and Morag Tong would put suspicion and resentment in the minds of the nords, who are not known for being very mer friendly.
In fact, I'd gander to say much of the dunmer culture we knew is pretty much going to change a lot. They're a scattered people, who have been abandoned (likely in their view) by their gods, the daedra and the Tribunal. They live in lands that are nearly a 180 from what they're used to. The fact the nords of Skyrim (not Solstheim, they're a different people) have yet to either kick them out or finish the job speaks how lucky they are, and how much they are being tolerated by the nords. If they began murdering each other and the people who are allowing them to stay, along with having a highly xenophobic gang try to push people around, it would only cause them to be weakened, and bring the hatred and resentment of the nords, who do not need that much pushing to kill off mer.
Oh, forgot to mention the MT is a religious organization. They kill to appease Melphala, and are more religious than the DB. The DB is a much more secular organization, in comparison.
Yes, you're right I forgot they went to Solthseim. However, I wouldn't be surprised if they overstayed their welcome and were forced to leave.
The DB is more money orientated.