I am about 90% sure that the SAA desk in the transit area will be able to issue a boarding pass - but if you're hand luggage only, why not just checkin online 24 hrs prior, and print your own boarding pass.
Three blank pages *should* be enough, so long as you can get immigration in ZA (transit, first time) to stamp on a used page - my Zim visa from last year is a full page, but they put entry and exit stamps onto the visa. You are supposed to have 2 blank pages for entry into ZA, so that would be fine. IME, they generally try to 'fill in the gaps' anyway, and if you ask nicely I would certainly expect them to do so.
[honestly, the ZA immigration guys have never checked for two blank pages in my passport, so the only danger would be SAA checking at VFA ->probably low risk anyway]