I think if you have heard nothing, you don't email. You normally don't get rejection letters until way later in the process, like the spring. If you don't hear within a couple more weeks, then you can assume you probably didn't get an interview.
If you had a phone interview and haven't heard anything, I personally still would not email after the thank you email. The exception would be, if you had another job offer, you could contact them to let them know that and ask if you're still under consideration. Or if there is a major update to your CV, like you get a paper accepted or a grant, you could also email to let them know that.
I know the lack of info is so aggravating. I think generally departments just don't bother to inform you what's going on unless you've had a campus interview. (Even then, I had a campus interview a couple of years ago and they never told me I didn't get the job.)