I flew DXB-CPT in J on a SAA codeshare emirates flight last August and was able to check in at T3 biz section and had access to the lounge.
The day before the flight I was able to access emirates Manage booking, select seats and then print off a emirates ticket (if I remember correctly the online check-in was not available though)
No tier miles were earnt, but I did get miles after sending in my boarding pass.