I haven't a clue how many people have Acrobat Reader. I'd imagine it's most. However, I find PDFs to be the bane of the web. If you have control of the project then I'd try to convert them to HTML as soon as possible.
PDFs are only really justified if they're specifically designed to be printed. There's something to be said for providing PDF versions of information that's primarily available in HTML, but not instead of HTML in most cases.
1. As with any plugin technology, you're excluding people that don't have it. Even 5% that don't have it is a lot of people on a significant site. Don't expect that people will rush to download the reader just so they can get at your docs. Most will just leave.
2. Acrobat Reader is a *different application* to a web browser. Obvious, I know. But confusing for most users who one minute are using IE (or whatever) and the next are using something completely different where all the menus are odd and even something as basic as scrolling works (or rather, doesn't work) in an unexpected way.
3. It's not necessary. Why make life more complicated even thinking about PDF unless there's some overriding requirement for it?
4. Opening Acrobat Reader may bog down or even crash older computers.
Jakob Nielsen has written about PDF here: http://www.useit.com/alertbox/20010610.html
He outlines when PDF is appropriate and how best to use it. I'm inclined to agree with him generally.