Your Pocket account requires a login, so the custom URLs that the service generates are specific to you and your account. Thus you can annotate them, but when shared, the URL won't resolve properly. At best those using the shared URL will get an orphaned annotation on a page that doesn't resolve. Your best bet in those cases would be to use the "view original" link in Pocket to go to the original web page which you bookmarked into Pocket and annotate that version which should be freely available to anyone you'd like to share those annotations with. (Pocket also doesn't mark up their pages with rel-alternate or rel-canonical links, so I think that Hypothesis won't be able to match them on the back end, which is another problem beyond the password issues.)
In personal experience, I find that Michael's solution works best for pdfs. Depending on the .pdf's source, I'll also often save it and modify some of the meta data so that the annotations in my feed have better Titles/authors and richer meta data so I can more easily search my account for them and identify them better visually.
Cheers,
Chris