Currently on MR #2 of 3 at JNB! While I am staying at a game lodge 2.5hrs north for 2 nights on this one, my next JNB MR is a literal same-day turn with BA 56/56 next month.
I haven't decided what to do.
There is an arrivals lounge Seksile (spelling?) that I use upon arrival. I think it closes at 12:30pm, though. I was thinking about then just checking in and hitting up the BA lounge as they have good food options there.
I have stayed at the Holiday Inn airport. They have a shuttle or an Uber costs $4. Room is nice and costs about $60/night.
I was debating just staying at the airport for those 13hrs, too. But I may leans towards another day at the Holiday Inn as I am an IHG Elite and could always use another cheap night in my stay history.
Also, the airside spa offers very cheap massages/facials/treatments. You could easily pass 4hrs in there.
The IC is also located at the hotel but I can't justify its expensive cost compared to every other hotel in JNB.
If you want an experience of a lifetime go to Lion Park. They will even come get you at the airport.

should take up half of your day but leave you with a lifetime of one-on-one interactions with baby lion cubs and cheetahs.

I was just there for my third time last week on my last MR to JNB.