point b: gotcha gaming. not sure what that is, actually. is my proposed solution of deciding how your universe works, presenting it, and then coming to a group consensus as to if everyone wants to play that way considered gotcha gaming? please elucidate.
I'm responding specifically to this point, because it's the point you've specifically requested further discussion regarding. If you'd like to discuss other aspects of your post, I'm happy to.
When NPCs - even major ones - spontaneously start having defenses against new toys, spells, and tactics that no witnesses outside the adventuring group lived to see, it's serendipity at best, 'gotcha gaming' at worst. Given a predisposition on the part of my past and present players to seek out their adventures in ruins, caves, and similar locales with a dearth of witnesses, my players tend to act surprised at best, outraged at worst when foes are already prepared for the party's best tricks, particularly when those tricks are relatively new.
...
If they are reasonably sure they left no credible witnesses a boss-type would tend to seek out or believe, AND they are reasonably sure that their magical defenses haven't been breached, they tend to become suspicious that the DM is simply engaging in gotcha gaming, where none of their attempts to secure a tactical or strategic advantage will bear fruit because the DM will simply metagame such advantages away.
I think this conflates the metagame restrictions with the in-game ones.
Shivering Touch was off the table not b/c its existence wasn't acknowledged, but as part of an essentially arms deal between the players and the DM. Players and DM being concepts that don't exist in the narrative of the story. In a universe where things like Shivering Touch, scry and die, and similar one-shot kills/incaps exist, intelligent foes would, it seems, make preparations against them.
* Such preparations didn't exist in your campaign b/c of the aforementioned armistice. Now, they (arguably) need to be reinserted.
In short, something like Shivering Touch might be new for your players, but it's not new to the world at large. You should contrast this with a creative twist, trick, or combo that the PCs come up with.
That being said, I kind of hate gotcha gaming. As a DM I tend to build my opponents with near total ignorance of what the players can do. I build them with general capabilities and, if I'm really on my game, with an eye towards their commonly faced foes. That is, my Mariliths are really good against other outsiders b/c they encounter them all the time, and mere mortals are rarely a noticeable challenge. Against a powerful, intelligent foe there will still be some gotcha-ness going on, but mostly by coincidence. My friend built a Marilith that was an awe-inspiring melee combatant and resistant to common magical effects. That screwed over some of our melee folks, but "melee" isn't really a unique specialty and her abilities made sense given her role and stature.
The only times I do keep an eye on my PCs' capabilities are to do the opposite of gotcha gaming: to give them a time to shine b/c I know they have some ability that will totally wreck this guy or encounter. Note, though, that my style of encounter construction does put the onus on the players. They are going to have to have enough counters and abilities to win the day. That's their job.
*Side note: having to avoid this kind of DM labor is one of the best excuses for removing various annoying abilities from the game. The same could probably be said from the players' perspective (e.g., what player wants to have to worry about scry and die?).