Waqar yes and Wasim wasnt caught but both of them, as well as many other bowlers around the world, did things to the ball that are probably not so common today. But this has to be seen in context.
Firstly, the law wasnt always so harsh. The cleaning of the ball around the seam with thumb nails was common from the sixties when I started playing cricket. One didnt do it to be able to reverse swing the ball (that wasnt even dreamt off then) but basically to keep the ball clean, to have a better seam to grip and bowl, and in the case of seamers/swing bowlers, to have the ball move around for longer .
This wasnt considered any different from polishing the ball which was done on the trousers and often after rubbing the surface under one's armpits to apply sweat. This was done openly and there was no 'wrong doing' attached to it. Just as spinners applied saliva to the ball. Tendulkar would have NEVER been censured for running his nails along the seam as he was and I am not sure it isnt a habit picked up in Mumbai where the ball would repeatedly need to be 'thus' cleaned by all fielders.
What was not done was rubbing the ball on the ground to remove the shine or scruff one side of it with external implements like a bottle crown. This came with the 'discovery' of the reverse swing, in all probability, by Sarfaraz Nawaz but definitely around his time.
This was taught by Pakistani bowlers to other Pakistani bowlers who followed and the rest of the world continued to flounder against this 'mystery' delivery. As they perfected the reverse swing, they also perfected the ways to get the ball 'into-shape' for maximum effect. Thus came finger nail and bottle crown scruffing (very differnt from cleaning or even maintaing the seam with the nail as was done by others).
I suspect the Pakistani's kept this scruffing bit under their hats not just because they thought it was cheating but , probably, more so because they did not want the opponents to learn the tricks of reverse swing and everything that went into achieving it including what I prefer to call 'ball management'.
The rest of the world, still struggling to come to terms with their inability to cope with this ball, jumped up and cried foul the moment they realised it was done by the 'differential' in the two surfaces of the ball. Since their own bowlers had not mastered the reverse swing till then, they wanted the 'underhand tactics' that managed the ball surface to be outlawed. I am not saying they were wrong but I am convinced that if English (or Australian) bowlers had mastered the reverse swing themselves and learned how to do it on their own rather than 'catching' the Pakistanis 'doing' the ball, they would have employed it themselves and it would have been left to the umpires or maybe some of the minnows to cry foul at a later date.
The point I am making here is two fold. One that it started with practices that were not scowled upon as they are today since they did not create any 'great' advantage in one side's favour and two, that the outcry would have been muted at best if the 'art' reverse swing had been 'discovered' by those who screamed 'foul' rather than them discovering only the 'ball management' part of it.
Finally, the denials of Pakistanis became much more strident as the authorities decided to outlaw 'ball tampering' by very stringent laws. I remember talking to Indian players long time ago and they all seemed to have been told by Pakistanis, with a wink, that this was their secret, when asked how the hell they managed to swing the old ball. Most of them (the Indian players) knew that one side was kept shining while the other was relatively rough. And they never, complained that it was illegal. That came much later.