Which formats does Apple Newsstand accept?
The Newsstand is just a special "Store" where you can download a 'magazine' app and the Newsstand itself which tracks the "issues" that your magazines have available

So your Newsstand app can display anything it wants in any format it can decode and display - an issue is just a big bundle of data and the magazine app is just an app that decodes and displays that data.

Apple don't give you any information about content formats as they don't care and don't specify.

PDF is a popular format as you can easily display PDFs on iOS using WebKit, indeed most magazines seem to use Webkit for displaying their data since it allows you to show a bunch of formats and it works well with embedded links.