Rode there via Mexico in 09/10 and never used an alarm nor disc lock, chain or anything like that. The last alarm system I used, the NON waterproof remote played up, so I had to remove it all on the side of the road.
Alarms in SA do not really work imho. You personally will be sick of the many car alarms that are going off every minute of the day, most people ignore them!!! You can buy cheap ones down there, people do and they are so sensitive, they go off for no reason, they are very musical though
I stayed in hotels, cheap as, usually less than $40, mostly around 20-25, and these had secure parking, or if not, the bikes were brought into the hotel foyer.
I never felt unsafe doing things this way.
Saying that, I do like the idea of a personal alarm that is NOT attached to the bikes system.
I sometimes used a bike cover, mine was big heavy and silver(the cover from rjays), so it took a lot of space, but I rarely used it.
I am now having made a dark(black, but dark green or camo would be better) cover made from RIPSTOP. This is light and compact, is waterproof(not that I care) and will just be thrown over the bike when I camp, which will be more often this trip.
Hope that helps