Well, some people believe that shiny colours are chosen by using inverse colours or opposite colours to the spectrum, but we can probably tell that this is obviously not true.
Shiny colours are simply just picked at random. The makers don't usually chose something that is too wacky. Most times, it's just something that makes the shiny Pokemon unique or just as well looking as the original one. But some Pokemon like Gengar, Glaceon, and Blaziken have the same colours, just a lighter or darker tone.
So, to answer your question, shiny johto Pokemon are pink/purple because that's what the makers chose. It could of been since many kanto Pokemon aren't purple/pink when shiny - but then again there's Pokemon like Gengar and Aerodactyl who are. So, there's no official reason why to why they're like that; it's probably just a coincidence.
Hope I helped! :)