That is a big fat myth, I don't buy it and I never will.
Firstly, its not New Zealand's or any other country's fault that the Springboks were not invited in 1987 & 1991. They knew what they had to do to get invited, and they wouldn't do it. The remaining teams can only play what is in front of them.
Secondly, even if they were in those tournaments it is no guarantee that they would have won either of them, and IMO, they would have been nowhere near. South African rugby was in a poor state at that time. During isolation, they did play a few "rebel" tests against second rate scratch sides such as the Jaguars, the Cavaliers and a much weakened England side (in all cases, many players chose not to tour or were forbidden to by their employers) and while the Boks won many of them there always needs to be an asterisk against those matches, due to the fact that they were against weakened teams and were controlled by hometown referees. We all know what a great record they had at home with their own referees like Gert Bezuidenhout, Ian Gourlay, Max Baise and Piet Robbertse. Then, when they came back out of isolation in 1992, when all the referees were neutral, South Africa found themselves well off the pace, losing six of their first seven test matches.
Thirdly, South Africa missing from 1987 and 1991 is no more significant than England missing from all the FIFA World Cups before 1950 and a few since. You dont hear the FA whinging that the 1930, 34, 38, 74, 78 and 94 World Cups didn't mean anything because they weren't in them.