Will the fact that my mother and I have different surnames cause some challenges in the future?

The long answer

I don’t think that it should be a problem, as women very often change their surnames after getting married. The fact that you use her maiden surname and she has changed hers does not make you any less her son. Your birth certificate should have her original surname on it. Even if you just had a clinic card recording your birth, it too would have your mother’s surname on it. She would probably have an ID in her original surname too, which you could ask to make a certified copy of if you were concerned that you might not be able to prove that you are her son when she passes away. 

It's always a good idea to keep important documents like birth certificates safely in case you need them as proof of identity, but I don’t think the fact that you have different surnames would be a problem.

You could also ask an organisation like Black Sash for free paralegal advice. These are their contact details:

Black Sash
Email: help@blacksash.org.za 
Helpline: 072 663 3739 or 063 610 1865

Wishing you the best,
Athalie