It's an occupied ruin, keep that in mind. People tend to build on top of what's around them and it could be a strange mixture of Dwemer and Nordic. That would make it look different from any of the other UNoccupied ruins.
This is what I was thinking too. Since Nords are living in it now, it's entirely possible that they built structures on top of the original ruins, or restored buildings that were previously in bad shape, and since it's Nords living there now, it's certainly possible that the new structures would have a very Nordic look to them. I don't know this, of course, since I haven't played Skyrim, but it might explain why the castle would look Nordic.
Take this for example. The British have a style of archetecture right? When they sent the first fleet to Australia and set the convicts to work making the cities, the architecture was VERY different, arguably un-British. (I live in Australia
)
It seems people find it rather hard to grasp that the same race can have more than one style of archetecture (Even though Morrowind was a prime example of this with the different Dunmer factions.) Or they don't want to grasp it because that would mean accepting that the Dwemer archetecture in Skyrim doesn't have to be an exact copy of what we saw in Morrowind.
What we've seen of Markarth doesn't look like the Dwemer archetecture I'm used to, but maybe in Skyrim, the Dwemer archetecture just looks different, if that's the case, I can accept it.