Word(s) to describe the emotion behind disappointedly looking over ones glasses?

A single word term fitting that definition is not likely to be be found in any dictionary; however, there seems to be no problem in finding two-word compounds. Here is one that would do.

• benign bemusement (with benign bemusement)

(This one is a rather well known collocation (ngram).)

Perhaps "askance" would aptly portray it as a "look of incredible disbelief" (Are you serious...?).

TFD - askance

There's no way to predict what emotions lurk in the heart of a speaker.
But if something is accurately describable as "disappointedly looking over one's glasses",
then I think there's no reason not to speak of "the emotion behind" it as disappointment.

Looking or peering over one's glasses is a non-verbal gesture for which there are no words — except to describe the action. The gesture conveys a sense of criticism, derision, or judgement. Body Language For Dummies describes it like this:

If someone peers over the tops of her glasses at you, don't be surprised if you feel scrutinised. Peering down on another person conveys a critical or judgemental attitude. The glasses underscore or highlight the action.
_{Source:Body Language For Dummies}

The good news is that while helpful, the glasses are not necessary for this gesture, or the gesture you describe that includes surprise and amusement. Minus the glasses, the adjective bemused (or the noun bemusement) works quite well here: a bemused look (a look of bemusement).

In addition to a sense of surprise and amusement, the word embodies a facial expression that expresses mockery or derision:

bemused adjective
3 : having or showing feelings of wry amusement especially from something that is surprising or perplexing

wry adjective
2 : made by a deliberate distortion of the facial muscles often to express irony or mockery

_{Source: Merriam-Webster}

See results from Corpus of Contemporary American English for bemused look. Of course, bemused has other senses too, so not all of those entries may apply, but here's one example:

28: And who can forget the bemused look on Ravi Shankar's face as he watched George Harrison struggle to control the sitar?

For reference, here is an image of something like what you described in your question:

Source: Memes Monkey

Putting it all together, perhaps:

He peered over his glasses with a bemused look.

 

Quite literally, one is looking down one's nose at the other person.

(Lexico powered by Oxford)

regard (someone) with a feeling of superiority.