Would love an all-time/yearly list! Also, I see a few comments criticizing the affiliate links. That's the reward you get for building cool stuff. No reason not to!
I think it's an honest mistake. The fact that you dismissed the popup seems to be stored in a cookie, so it bothers you only once ever (twice if you use the back button).
Sidenote: since I'm in the EU I think you need to need to ask me for permission, but let's not open that can of worms.
Indeed, get rid of it, your site design is so sparse it's hard (I think) to miss the "Newsletter" item at the top. Or put it inline somewhere else, e.g. at the bottom of the list, if someone's bothered to scroll down that far the odds they're interested in the newsletter are quite a bit higher, I'd think.