What is one trying to say by simply responding “Naja!”?
When "simply responding Naja", that can be for closure of a (possibly but not necessarily unpleasant) topic. You'd lower your tone here.
Naja.
as in
Let's leave it like that
It can be used to announce an objection or a further thought, too. In this case, however, the intonation is rising. and it must follow something (objection/thought)
Naja! [..]
The objection/thought necessarily has to follow.
Another use case is for closure of a somewhat unpleasant topic. You'd lower your tone here.
Naja.
as in
Let's leave it like that