I use Safari and Firefox mostly, and haven't yet run into any of the issues you bring up - pdftotext gives me full text search with ease. All the links still work, PDF's are easy to read (assuming the page doesn't do weird layout tricks), and for the worst case, I at least can search my "bookmark" PDF archive and go back to the original live web page if needed.

Looks like Apple's implementation is a bit better then. I just tried on Windows and I definitely don't get any clickable links when printed with the OS print-to-pdf driver. (I do get them with Chrome's save-to-pdf feature which circumvents "printing" and generates the PDF itself.)

Good to know for future discussions about this technique. I wonder if there is a way to make Chrome on Windows behave better in this regard .. seems quite shortsighted to me that they'd remove the links, although maybe a security boffin has made the case for it.

Either way, haven't used Windows in decades, so its a non-issue, but it is interesting to note that this isn't something I'd be doing if I did switch.