The orange fireball easter egg is still in Hyper Fighting?

Yep. Capcom left it in, although at the time of release most people knew there was no proper method of doing them. In the next version of the game, Super Street Fighter II, it was removed -Ken's fireballs are always blue and Ryu was given a new orange fireball special move called the shakunetsu hadouken.

Are there are differences between the Japanese and USA/European versions?

The usual changes apply (Japanese version has more win quotes and different names for some of the bosses) but the major difference is that the game has a different title in Japan. It is known as Street Fighter II' Turbo Hyper Fighting over there, everywhere else got rid of the word "Turbo" in the title. However, the SNES version put the Turbo back in the title no matter the region.

Why was the SEGA Genesis port called "Special Champion Edition"?

Apparently it was because of Nintendo. Nintendo apparently paid Capcom for exclusive rights to either the game or the titles "Street Fighter II Turbo" and "Street Fighter II' Hyper Fighting", so only they could use it. To get around that, Capcom just changed the name to Special Champion Edition for the Genesis version, even though it still includes all the extra moves and speed from Hyper Fighting. In Japan, the Genesis version was released under then name of Street Fighter II' Plus.