When should I reply "thanks" to a professor's email?
Summarizing all my comments as an answer,


  I am not sure if I should reply with a simple "Thanks" or if I should
  just let it be.


It depends on the number of students the professor wrote to. If it is an invidualized e-mail for a limited amount of people (apparently your case), yes, a little "thank you" is the nice and polite way to go. (On the other hand, if the class is a huge auditorium of a hundred people, the professor probably doesn't want this amount of e-mails arriving in his/her inbox).


  Also, the email was sent about 6 hours ago if that matters


6 hours, 24, 48, it doesn't matter. E-mail is not the same as instant messaging, and it is generally okay to skip a few days - especially in your situation: the professor is not waiting for your answer, it's just a nice thing to do, but if you wait three days or don't write at all, noone will notice.

Just write "Hi Professor X, thank you for taking the time to notify me!" and that's it!