It's been a while since I read the books, but I don't think Howland Reed would necessarily be known to anybody at King's Landing, and in any case 20 years of hard living would have changed his physical appearance a lot. In the books, he lived in the middle of an area a bit like the Fens in England before the Dutch came over and drained them a few hundred years ago. I think it's a bit to the north of the Twins, and so falls in the North, ie Stark territory. The people there are odd and don't mix much. Howland Reed came out to serve in the war with the Starks, because he was Ned Stark's bannerman. At the end of the war he went back into the bogs and hasn't been since.
In the books, Jojen and Meera just turn up at Winterfell because they somehow know that Bran needs them. HR sent them, or agreed to them coming. We have no idea what's happened to him. Before the Red Wedding, Robb Stark sent a couple of people off to find him (one of them being a Mormont woman), which I think was with a view to getting him to bring his people into the war. That's still a dangling loose end in the books, IIRC.
It had never occurred to me that HR might be HS, but I rather like the idea now. I wouldn't put money on it, but who knows? Almost anything is possible in GOT.
I may be alone in feeling this, but I've really enjoyed series 6 so far, more than series 5 at the same point.
And finally, I am proud to say that I did indeed work out that R+L might =J from reading the books! My theory now, though, is that that is a bluff and the truth may turn out to be a bit different.