Last 3 trips thru JNB in the last 18 months via Delta/SA Airlink, the SA Airlink agent, checked us in for the SA Airlink flt then we had to go over the the separate window and get in the queue to pay the extra fees. It was that window that actually printed our boarding pass.
Coming back from WDH last Jun and all other several dozen trips I've made there, you check in, your luggage is tagged and set behind the counter. You will be given the baggage routing tag to take with you to the NAMPOL office, clear your rifle out of Namibia. The NAMPOL will stamp the routing tags and you'll put it on your rifle case and carry it back to the check-in desk. On the way, back you'll stop at separate window again to pay the rifle transit fee and any overweight bag fees.
From there, you go back to the check-in queue, (you'll have head of the line privilege) show your payment receipt and they will issue your boarding passes.
Yes, both JNB and the WDH fee offices take CC's.
Side note regarding ammo - From the US to JNB is is possible for the locked ammo box to be inside a regular checked bag. I say POSSIBLE because I've done it with several and those same airlines have also required me to take it out. I was not charged an extra fee. On all of the occasions I was allowed to leave it in my checked luggage AND that bag was checked thru, it went all the way thru, with ONE exception.
In 2019, first trip to Bots. Luggage, with ammo case inside, and rifles checked all the way to Gabs. Delta/Air Botswana. When we checked in with Air Botswana the next morning, they had us go down into the luggage transfer area and remove our ammo cases from the checked bag. They did tag it to Gabs and it pitched up just fine there.
On the June 22 trip to Namibia, my friend who checked all the way to WDH had his ammo in his checked bag and it went all the way thru. I claimed in JNB and when I re-checked the bag and rifles the next morning, I had to take the ammo case out a the check in desk. Same deal, they just tagged it and no extra charge.
In 2020, I flew to Bots twice on Qatar Air. Going over, ammo was in checked bags all the way. Coming home, Air Bots checked our luggage and rifles all the way home with some left over ammo in the case, checked separately but would only give us boarding passes to JNB. When we checked in with the Qatar Air desk, they wanted to charge me some crazy extra fee for the ammo (something over several hundred USD for 50 rds of 30-06. I told them keep it, I wasn't going to pay the fee and as such now they would be in violation of RSA firearms laws by being in possession of loaded ammo that they had no permit/license to possess. Told me "you must pay the fee". I told them was only required to pay the fee IF I wanted to bring it back. At what you're charging me, I don't want to bring it back, you deal with it. They put it on the flt at no cost and it did pitch up in Boston where we entered the US and cleared Immigration and Customs.