The runes blocked Shagnasty, but not the Denarians, Harry, the Archive, or the normal humans. The Denarians were probably as bad in intention as Shagnasty was, and the Fallen were probably at least in Shagnasty's league of power, if not beyond. Maybe the runes only block supernatural creeps who don't have souls?
The Warden question came up again in the Pre-GS thread, too, and it was noted that while the Warden apparently had something to do with preventing Shagnasty from using the Nevernever to travel to the island, the two human-seeming people were able to do so, and they were able to bring fae creatures through with them.
Two possible explanations for this come to my mind: First, that whatever is blocking Shagnasty from using the Nevernever, fae creatures are exempt from it. Or second, that once a portal is opened, any creature can pass through, even those who would be blocked from entering on their own.
If the second explanation is true, then the same magic which empowers the runes on the cottage and the tower may be what is blocking entrance onto Demonreach from the Nevernever. The wards around the island might prevent anyone who doesn't have a soul from entering the cottage or the tower, or from even opening a portal onto Demonreach from the Nevernever. Very human-centric magic. And maybe good for Harry, defense-wise, if he decides to move out there.
Still, I think this is only one of many equally likely possibilities.