You have to have an invitation letter from your outfitter in Namibia regardless of whether you go through JB or not.
I've been to Africa 3 times, so I'm hardly an expert. However, take some friendly advice, FWIW of course.......Call Steve Turner at Travel With Guns, have him book your flights, have him book Africa Sky guest house and buy their VIP service which includes meet and greet at the airport, SAPS gun permits, a fantastic steak dinner, fantastic breakfast, clean, spacious rooms, and all the beer you want at your disposal. This costs around $275 IIRC for the whole ball of wax.
Last year I did the above. The AS guy met me in the arrival hall, took me to the SAPS office, and after a couple of other hutner's quickly got their rifles, all came to a standstill. There happened to be a shift change in progress, and since it is indeed Africa, the whole process stopped. He whisked me off to some office where the nice lady confirmed my rifle was indeed made it to JB, so back to SAPS we went, where approximately 12 others were wondering what the heck was going on. My guy was having a conversation with one of the SAPS guys, and off behind closed doors they went, and in 5 minutes they were back with my rifle, which was immediately cleared, and off we went. The other dozen guys were still standing there helplessly. Turns out, the shift that was leaving just left all the rifles out in the back somewhere for someone else to sort out, and the guys up front could have cared less.
The whole "ordeal" lasted probably 45 minutes total, but I was off to Africa Sky with my rifle to eat steak and drink Tafel's while everybody else was still trying to figure out where their rifles were. The choice is obviously yours, but I'll use Africa Sky's VIP deal every time I go, and am doing so again in August.
Oh, the next morning after breakfast I was taken "by the hand" by the AS guy back to SAPS, checkin, etc, no questions asked by anyone, nobody with SA Air asked me about ammo, or to check it separately like they sometimes do, nothing. Everything went off to perfection, no hassles. I feel it is well worth the cost.
Namibia is painless, but you will have to have your paperwork in order there too, but it is very simple.
