The thing about Wraith Fever been spreas by the Ratkins was something I forgot and could actually happen since in the Basement there's a scene of a Ratkin fucking a Bareshade guy, so, yeah, maybe.
I don't know exactly if it was a coincidence or not, but right after I gave Bernard the Spectral Sirup and ended the Shopkeeper Sickness event, I unlocked the Rat Problem event. Maybe there are connected after all.
I never noticed Bernard's gem and that's a interesting point. Maybe in the future we could unlock a dialogue which we ask him about it.
About the Nameless and the shapeshifters, I totally disagree with you. The game is very clear when they talk about werewolves and shapeshifters. Never once I know they used both as synonimous. When the game talks about werewolves, they use exclusively the "werewolves" word. Same as the shapeshifters.
I believe Nameless was telling the truth, since he seems interested in what we are doing and just gave us this hint. My strongests guesses are Feliar (since I saw that message about him on the cave I never ever trusted him again. I don't really think Victoria would be craving messages in stones walls, she has more interesting stuff to do anyway), Hayden (He is the newest member of Bareshade from what I know and he said that he moved to Bareshade, so he's not from there and the fact the he never mentioned Northcrest or were he came, it's kinda strange.) and Bernard because, as you said, he's probably hiding something from the MC.