1) missingno is present in all gen 1 games, but he's really only able to be encountered in a normal playthrough in the translated/localized copies. most nips have no idea what missingno is
2) jap video game culture doesn't like to make light of glitches/errors in gaming. it's an alien concept now, but when you spend real money on a product you expect it to work as intended, so if there's a glitch in a game they've let you down. nintendo is particularly strict about this standard of service, so while they're happy to make jokes and references to easter eggs and developer secrets, glitches aren't kosher.
mew was to japan what missingno was to US/intl markets in terms of infamy at the time they were discovered, respectively. so in a way, they did 'canonize' the surplus programming, but it was the one they were familiar with and intended for
