Whoever did the searching before did a very good job, as these were the only two messages I found and I spent a lot of time trying to cover every inch of the world. Plus they were kind of hard to see because of the colors of the floors they're on. If I still missed any, I doubt there could be more than 1 or 2 left to be found.Blighttown:
Shortly after the upper bonfire, on a ledge overlooking the Parasitic Wall Hugger.
The Duke's Archives:
In Seath the Scaleless's first location. To the left after you pass through the fog gate.
I would also remove three of the Catacombs messages from the list. "Treasure", "Up", and "Shorcut ahead" all display without the use of seek guidance, so they're non-hidden. I'm unsure if they may have been hidden upon release or before a certain patch, though, but they're not hidden now.
Same goes for "???" in the Crystal Cave. Actually... I can't find the "???" message at all anymore! I do remember it being there, but now there's a non-hidden message that says something like "Path ahead", where I think "???" used to be. This might've come with patch 1.06.
I couldn't find any hidden messages in the DLC areas, which makes me think that "Let the be light" and "If only Hawkeye were here..." were probably intended to be hidden, but then they gave up on it. Perhaps it is indirect acknowledgment from the devs that seek guidance was mostly pointless...