The practice does seem to have been deprecated, but there were a couple of advantages to having embedded PDFs - for some people in some situations.
When Acrobat became a widely used documents publisher in business situations, it offered the opportunity for less technical admin to distribute and share multi-format information, and with the added bonus of having an easy way to publish to the web.
Embedding the document in pages allowed the adding of pages to the document without having to structure new navigation into existing pages. True, all of that could be done by simply referencing the pdf as its own page, but that cut out site navigation from the page.
Embedding allowed a main navigation system, with the another added bonus of having a multi-page search facility within that document, multi-page document printing and image zooming independent of the whole page. It was like a bargain-basement CMS system.
In fact, adding a multipage search facility to flat pages still can't be as easily implemented with newer (compliant) web methods. Just upload it, and it's indexed and searchable.
It can still be done (by embedding in flash) and there are any number of websites claiming to tell you how to do it, - but nearly all of them refer you to online services who will convert and keep your document and generate the embed code for you to put on your page. That is probably the best solution for vendors (hi, vendors).
An alternative is to find an old Macromedia suite that has FlashPaper in the package, that will convert your pdf to flash and you add it as flash or flashpaper in Dreamweaver. I doubt that it works on all platforms and browsers (although Adobe still sell it per site/licence). I think it only installs up to Win XP (and not at all on Mac).
FlashPaper with MenuWriter seem to co-exist if you set the z-indexes [Example]