There are already a lot of answers posted, but I still feel compelled to make a point I don't think anyone else has:

**It's probably not meant as a question, just an observation.**

The manager could have also said "There's no one else here, huh?" This is not really a interrogative sentence, question mark or no. This can be seen as a form of small talk, or even just your manager talking to herself in a way. You can respond with "Yeah, I guess so" (an equally unnecessarily observation) or "Yep" or nothing at all. This is just a normaly way humans express themselves (surprise or frustration that no one else is in attendence, for example). Don't get so hung up on how to respond to this non-question.