Not everyone that plays chess, plays on chess.com and not all people from a country join a group for that country. Some players don't join any groups.
A slightly better search would be to do one on location on the member list.
I have no idea how accurate it is but I just completed a blank search using South Africa as the country and it returned 2,566 pages of members. If you assume the query is correct and the pagination count is also correct (can't verify that easily), then you get approximately 64,150 accounts that have chosen that as their location.
Many of those are probably not active, some may be duplicate accounts, and others have that as their location but may not have any ties to the country at all.
So I did a calculation - Chess.com says there are 13,725,797 members on this site. The official South African Team has 922 members. That is like 0.000067172% of the total, which is an extremely small ratio. So where is everybody?