Just reiterating some points here:
If it suits the story, then sure, in a university of sages (one can assume the professors are at least fairly "high level" -obviously :high level" means different things to different systems and campaigns.) So your options are, as stated:
1) Let the NPCs run the ritual, "off camera" as it were and provide them with a location.
2) NOT let them run the ritual. Either because a) it is waaay too expensive for the university to even consider, if you chart/keep track of such things, b) While the professors are very capable, there actually
isn't anyone high enough level to cast it...in a university of sages though, this sounds weak/flimsy to me if I were a player.
3) Have the ritual (on or off camera as you prefer for good -or just plain convenient- storytelling) and not get any results...
3-i)...or only get partial results ("We only know they are to the north")
3-ii)...or get faulty results ("They're in the parlor with a knife."..when they're actually "in the kitchen with a candlestick.")
and 4) My initial reaction when I read the OP was simply, "Isn't there some way the abductors (or those that hired the abductors) would be able to defend themselves against scrying? A counterspell/ritual, non-detection? misdirection? Some mystical "gaudy broach against scrying". Even just something with a limited charge, like "It'll foil attempts at divination 3 times before becoming just a normal gaudy broach."
That way, the NPCs "tried" and were "blocked". They'll be ticked at the unfruitful "waste" of resources (and what sounds to me to be
massive amounts of gold, again if you keep track of such things).
You didn't tell the PCs "No, you can't." to their perfectly logical request, which should keep them happy while at the same time maintaining story integrity and leaving it up to them to figure out...at their level.
Now to the actual point of the post, as a DM, if the resources are there (in a given town or city, temple, what have you) then sure the PCs can try to gain access to it. I do like to try to maintain some internal world consistency.
For example: If I tell the party (or more likely, they find out by asking around town) that "this city contains the high/greatest temple of the goddess of magic in the known world", I can't then say "Nooooo, they don't have any magical resources you can use."
Of course, maybe the head cleric is a big jerk who reserves his magics for his "local congregation" not wandering passerbys. Or insists that only devout worshipers of the goddess are permitted access to the library (but some acolytes can try to look things up for you if you wish...with a reasonable donation of course

Maybe the "really sacred magical tomes and scrolls" (i.e. high level spells/rituals) or truly "arcane" histories and documents are for the highest level of the clergy's eyes only, period.
Simply because a resource is there does not mean the PCs automatically have access to it...even if it is logical they should ask for it.
Now, if the party then undertakes some endeavor to try to win the high priest's good graces...side-adventure fun time! And it might get them somewhere.
I suppose the overall POINT I'm rambling on about is this:
As logical as PC requests can be, there are plenty of equally logical reasons a DM can come up with to limit (or flat out refuse) things the DM feel should be beyond the PCs reach without disrupting the story or immersion.
Good luck and happy gaming.
--Steel Dragons