Hi Charl,
early to mid winter will still see smuggling activity, so you will do well to avoid camping directly at the summits of Mweni, Rockeries and Ntonjelana Passes. As for the shepherds, they will now generally start moving away from the escarpment, but there are always still individuals around. I have encountered Basothos in mid-winter right across the escarpment, even in snow/ice conditions. While not all of them are a threat, it is always good to bear this in mind and not assume that you are alone.
Ifidi Pass is a good place, in particular Ifidi Cave, since it is really out of the way and difficult to find (don't be fooled by the shallow overhangs often mistaken to be the cave). Fangs Cave is an excellent cave, tucked away in a gully, not particularly easy to find and certainly not frequented by the Basotho.
Ledgers Cave and Mponjwane Cave are classic overnight spots for this traverse and are also pretty good from a security angle.
Between Rockeries and Nguza Passes is a quiet little valley where you can easily find solitude and watch the vultures circling around the cliffs overlooking the Rockeries. Nguza Pass is a very nice place to camp - it does lie along a busy shepherd route but I've never heard of any problems there.
Twins Cave is a classic spot though it does get used by the smugglers and cattle rustlers. Though they also use the nearby annexe cave, this is further away from the trail and a better option between the two. More secluded alternatives would be Easter Cave (which is better shelter anyway) or a cave which I refer to as Bellevue Cave, on Mlambonja Pass, near the split leading to Twins Cave.
Bear in mind that Bell Cave is right on the trail. I've heard of one security incident which happened several years ago. If this bothers you then rather camp on the grassy plateau on the other side of Cathedral Peak.
Hope this helps.