Do you end a sentence in had?
The final "seen" is implied because it's the same verb used earlier and the sentence is structured as a comparison[1]. I think it's correct either with or without it. Including it sounds a little more formal to me, omitting it a little more colloquial -- a stylistic choice. Also, you would include it if there were any possibility of ambiguity, which doesn't apply in this case.
[1]I'm not sure "comparison" is the right term for this, but whatever it's properly called, the structure of the sentence indicates the same verb is used in both clauses.
ETA: I think I'm wrong about it being a comparison. You could just as well say "They hadn't seen what she had
done." Or "They hadn't seen what she had
eaten." In cases like that, you can't just end with "had". The verb is different, so you have to specify it. The reason "seen" can be omitted in the original question is
because it's the same verb.