Hi,
HTTPS is in plans. Actually, @watcher already gave me a SSL certificate, I need to recall what the problems I had last time with it and we can cover some important bits with it.
LetsEncrypt is a good step forward and I really would like to use it instead. So far there are quite enough of success stories, highlighted problems and alternative tools, so that wouldn't be a pathfinder problem.
As for GPG, this is a question for core dev team. I think it's good call to sign Miranda NG binaries. IIRC Windows provides own way to sign executable/files, but I'm not aware about cost of that feature and how it works.