Well, I'm understanding how the game works a bit more after some additional playing. For reference, I'd opened up about ~300 free chests. This leads to some very skewed numbers like 40 Smiths against the base 3 Cures.
At the time I made the thread, I was unaware that cards from the board game were limited to their original quantity, and that all the treasure cards were new additions.
What you say seems to indeed be true, in that the treasure cards only seem to take up a percentage of the current playthrough collection, I still find it odd that I've found over 10-20 Beast Skins/Smiths and I've only one Augury, for example, when there should be two from Deck B (and a third from C, if I'm not mistaken?). The same with the Deathbane Light Crossbow +1. Maybe I had discovered another copy of Augury early on and sold it, but I think that would still leave it available to be reintroduced, no? Anyway, I also remember seeing Shalelu and Sheriff Hemlock once, and either failed the checks or sold them, but I've never found them again either.
HOWEVER: Now that I'm actively looking for them, I have found quite a few copies of original cards, like one of two available Hastes, and Father Zantus. So I'm not sure if there's a problem or not, but I think there may indeed be some skewing from the treasure chests, especially because I'd opened a ridiculous amount.