In the first sentence, it depends on how you're using "then." If you're using it to show sequence (the second example below), I'd definitely leave it out. But if you're using it as in the first example, it's optional.
A: She called to ask you about the homework, didn't she.
B: No, that's not why she called.
A: It isn't? Well, what did she want, then?
VERSUS
A: The first month, she wanted a mink coat, then a set of pearls... and the next month... you won't believe it!
B: Good heavens! What did she want then?