I've also just taken my ammo in after-market plastic boxes "sealed" with duct tape, and never had anybody question them.
In fact in multiple trips to Africa, often with airline trips within the same country, I've yet to encounter any consistency in what's supposedly the correct procedure. I try to find out beforehand, but what I've been told and what's actually occured haven't always coincided. And not just with ammo either.
One friend who was flying within South Africa went to Kimberley on a South African Airways flight, with two rifles. When he checked in for his flight on a SSA feeder flight to Port Alfred a week later, with the same two rifles, he was informed they didn't allow anybody to fly with rifles as luggage. He had to charter a flight to PA.
As is often said over there, "This is Africa.