I was also in Namibia 2 weeks back and had the same problem with only 7 hookups on 18 runs.
I was fishing biggish baits up to 65cm kob that were flapped as I was looking for bigger fish. I also fished Kob and Galjoen heads and I fished Mile 8, Mile 30 and Mile 68.
I let them run 50m on free spool then struck, I held tight on the take and struck hard. I pulled up tight on Circle hooks etc, etc, etc, etc.
I had chance to inspect every bait used when I missed a run. What I found was that the sharks were not gulping the bait down but were biting the bait and swimming off with it in there jaws.
It's as if the sharks were tentative and were mouthing or testing the bait and not eating it.
I spoke to Simon McGowan of Sea Ace tours and he was experiencing the same thing. What he added was that there were plenty of baitballs off the coast (seen while snoek fishing from the boat) and the Sharks, Snoek and Seals were hammering them in the morning so it was possible that the sharks were just not hungry.
With this information I changed the rig, I put a 3/0 skelm hook onto the trace, this I hooked into the roof of the Kobs mouth so the hook was holding the bait only (didn't go through the head) and not to hook the shark I then threaded the 12/0 Denso through so that it was hanging fully exposed below the bait - result was 4 hookups on 4 runs.
What you explained is the method applied by 99.9% of Shark Anglers and in general angling would work fine but the Bronzies particularly were full of SH-one-T over that period.
The sharks that I missed, where there were no teeth marks on the bait were in all probability Hounds and Spotties that struggled to get these baits in, I then left those baits longer until they could get the bait in or that they fiddled long enough to get snagged on one of the hooks.
I don't think you were doing anything wrong but situations and conditions made for more frustrating angling than normal. The water was also a lot warmer than would be expected at this time of year it was 21 degrees at Mile 68 for example