There is also House Sotha of which Sotha Sil is the last living member. Back in the day some people refered to the Dwemer as House Dwemer. There are probably far more minor houses, but they are all of little importance as they don't get politically involved, are pawns of a Great House or have just too little influence to be noteworthy outside their community.

If we assume that every Dunmer family that had any importance was a house itself, then the ancestral tombs of Vvardenfell (probably mainland Morrowind too) could give us an answer. I don’t know if there is a distinction between house/family in their culture though. Even if there is, it’s hard to tell where the boundary is between the two.

I would not say we have a definite number for the amount of non-Great Houses, there may be a hundred, a few hundred, who knows. Though they would be shuffled into the Great Houses either as part of the Family line (Little branches off from the main family line) or said House is under that Great House as part of an alliance (Ex. Sathil from Infernal City). An independent House would be an interesting thought though they would be less likely to remain that independent for a long period of time.

Minor Houses (family names) may work as vassals for greater Houses

Right there, we can deduce the Llothan name is vassal to Selos name, which in turn, rely on one Great House at the top of the hierarchy