Is generic "thank you" email a waste of time in academia?

If you send a thank-you note, in addition to being polite, you let the professor know that you received their email and don't need anything else from them. That lets them avoid trying to follow up with you later.

A thank you for a quick response is usually appreciated to show that the time spent was worthwhile. It makes people feel better. So there's absolutely no reason not to send one, if you so choose.

The formality of your email should be relative to where you are: if you expect formality (as in Germany), you'd still include the "Dear X" header; in places where it's less formal, such as many US universities, you can dispense with the salutation.

Professors receive hundreds of emails every day. Adding a dozen thank-you emails won't help them to scan their emails for stuff they need to know or need to answer.

I'd propose to save the thank you for the next time you meet them in class or on the hallway. Still polite, but not a waste of their time.