One great thing about the Haruhi franchise is that it leaves enough unanswered questions to keep fans guessing, and the shippers happy. The events of the final chronological episode in the first season, the embarrassing things that happened during the underage drinking in Remote Island Mystery (which was completely omitted from the anime due to obvious reasons), Adult Asahina’s coquettism to Kyon, etc. One’s mind could run amok trying to make light of these things.
I think that’s a great thing, encouraging the audience to interpret the subtle stuff for themselves.
Now, about the after-credits scene in the Disappearance movie. Did the sight of boy helping a girl apply for a library card make Nagato happy? Is that a smile she’s hiding behind her book?
To me, the answer is both yes.