I do the same with most of my AI and AIS lenses (the screws on my AI 50/1.8 are too tight to get out). In most cases you can replace the screws with no problem - the lenses look better with the chrome screws heads than with empty holes. In some lenses, such as the AI 400/5.6*ED and AIS 50/1.4, the screws are too long, they will bind against the inner barrel and effectively lock the aperture ring. If you decide to replace the screws, take care as you tighten them, if you feel any resistance or the aperture ring no longer turns freely, take the screws out.
To get around the problem, the previous owner of my AI 400/5.6 removed the prong and padded out the screws with a short strip of metal like the base of the original aperture prong. I have seen lenses for sale (ebay) with no prong where the chrome screws are replaced by shorter black-headed screws. These must be the screws used by Nikon Service that Akira mentioned, I'm not sure where you can get these screws from.