PDF password protection is indeed (usually) rather easy to get around. Simply by opening the PDF in any third-party viewer other than the official Adobe Reader, you can usually circumvent all the restrictions, including printing (plus editing, page extraction, etc).
Taking a quick look at a handful of files, I believe the BAA has used various different security settings when preparing Journal PDFs at different times. All the ones I’ve looked at do allow printing, but block other actions. I could well believe that some might have restricted printing – presumably unintentionally.
It would be interesting to know exactly which PDF files are giving you trouble, though in the short term it will probably be much easier for you to circumvent than it will be for us to fix.