Haven't managed to find them with stock, building menu nor level <_< Weren't each 16x16 tile supposed to have one? Or is that changed? Or am I just missing the one tile every time due to not being able to embark 16x16 anymore and I'm just really good at missing one tile when embarking with smaller locations?(10x10 or 11x11 seem to be largest fortress game can handle, though latter still sometimes crashes the game before embarking and former crashes game while in fortress mode)
In the previous version, Word of Toad was that there was exactly one per 16x16. Which means that if you copied the save, embarked on an 8x8 of one quadrant, used one of the methods to detect it, and repeated three times for the other quadrants you were guaranteed to find it.
At this point, there are a few options:
A) User error(s). They are there and detectable, but no one has gotten it right. Evidence is building that this isn't it.
B) They are there as before, but some or all of the methods to detect them shortly after embark have been fixed. (Most of these methods were technically bugs.)
C) They are supposed to be there, but one of the many changes has broken them.
D) They have been removed, as the new Dark Spires, special holy materials, etc. supersede them.
I would not be surprised by D) as it makes sense that the previous generation's special subsurface sites were a simplified prototype to the more elaborate system in the new version, which directly connects into the world mythology. That said, it is entirely possible that it's one of the other options is the case; doing some Science! with multiple types of detection method would be useful, especially if it turns out to be B).