Correct me if I am misreading things, but isn't the sun actually a hole to Aetherius through which magica enters Tamriel? If this is the case, why is it harmful to vampires?

Because tropes, I think.

I still say Vaermina has a good amount of influence in this curse. Why Vaermina? Vaermina is all about nightmares. Nightmares occur when people are dreaming. People dream when they sleep. People sleep when it is night. Vampires are nightmarish. Vampires operate in the night when everyone is asleep.

THEORY:
Aetherius tends to be more Anubic, while Oblivion tends to be Padomaic. Vampires, being of Daedric and thus Padomaic origin, cannot stand Anubic power.
They thus are also mildly hurt while outside during the day, but less so.