I don't know about an official branch, but they do have JWs in contact with HQ. They contacted me in Cairo when I lived there-by phone. I wasn't interested in talking, but they wanted to meet.
I don't think JWs are that hidden. Coptic Christians are at least 10% of population and the state has funded museums in Coptic district.
My Arabic teachers were openly Christian and taught primarily foreign Muslim students. Christians are not rare or normally singled out for special treatment in Egypt, officially or otherwise.