While we examine the issue, two things to keep you going:
as you noted, you can switch to a different PDF reader that supports deep linking (there’s also the free Skim app).
Hook’s deep PDF links explicitly encode the page number of the destination , such as page 7 inhook://file/50jHOw3gJ?p=cG5sL3Rtag==&n=Anderson2002.pdf#p=7&x=39.540199279785&y=237.253799438477 (p=7).
Also, Copy Link does work in PDFPenPro under macOS 12. And one can open regular links. The question is why are the deep link invocations not working. I’ve now noticed that independently of Hook, GateKeeper seems fussy in macOS 12 when switching default PDF readers (to whatever PDF reader, not just pdfpenpro.) We’ve been in touch with the developer (Nitro) and we will revisit this tomorrow.
There is definitely something odd about deep linking with Monterey
I had this working stable for a long time on PDFPenPro. Now I am unable to create a deep link in PDFPenPro and then go back to it with that app.
Interestingly I switched my default PDF reader to Adobe Acrobat Pro DC. I was then able to go back directly to the links created in PDFPenPro, but I am not able to create new deep links within this app.
We’ve identified an issue. macOS 12 has difficulty with some bit of AppleScript which works fine on prior versions. We’ve developed a work around. We hope to release it today to the script server.
(We’re getting reports of other AppleScript issues with macOS 12 from people who had installed the beta, which we had too. it may be this one is related to that. )
Version 185 of Hook integration scripts is now available. This includes a fix for an issue that could prevent deep links to open properly in PDFpenPro under macOS 12.
2. Hook’s Automation permission to control the app is effectively disabled
the skim app never showed up on that list of “privacy-automation” for Hook. Now I also remember that when I first time used Skim, it did not trigger a reminder like other apps do.
Maybe that’s the cause of the error? I did uninstalled both Skim and Hook before restarted my computer and re-stalled the two apps again but it still didn’t work(skim not in automation list for Hook and no deep linking). Is this a bug from macOS 12.1?
since this topic of the OP was PDFpenPro, and that is fixed, I’m closing this topic. I’ve started a new topic (macOS 12.1 AppleScript issues affecting Skim ) for discussing the Skim - macOS 12.1 AppleScript glitch. (latest seems to be that the Skim PDF app developer has raised an issue with Apple.)