Und dein Onkel, wann siehst du ihn wieder?
Why is this sentence Nominative?
Isn't dein Onkel a direct object? So it should be Accusative?
These are two main clauses, connected by a comma. Let's have a look at the first clause only:
Und dein Onkel?
This is short for:
Und was macht dein Onkel?
And how's your uncle (doing)?
Clearly, the Onkel is the person doing something. That's why he's in nominative.
Nobody would write a sentence like this. It is typical of a conversation, where the speaker first remembers of the uncle and having already spoken the first part tries to bring it to a somewhat consistent conclusion.
So a more convincing interpunction would be, as Janka mentions:
Und dein Onkel? Wann siehst du ihn wieder?
Note, that ihn is exactly that accusative, which you correctly expect. The first part is still incomplete and could be imagined to mean something like Wie geht es deinem Onkel?.