In a conversation with Kiwi Talkz, Metroid Prime developer David Kirsch – AKA Zoid – has confirmed that this rumour is actually true. Kirsch reveals that he only actually played Super Metroid after being assigned to Metroid Prime, but loved it so much he completed it twice in 3 days.
Because he was such a fan of the game, he managed to get it loaded into Metroid Prime, as per the rumour. He also confirms that it was indeed the unofficial nature of the emulator he was using that caused Nintendo to ask for its removal – but Kirsch says that his efforts were what ultimately led to the original Metroid being included instead.
During the same chat, Kirsch – who was referred to by Shigeru Miyamoto as 'Zoid-O-San' – reveals a few more pieces of information relating to Metroid Prime's development. For example, when Miyamoto saw the first prototype of Metroid Prime, he immediately spotted something wasn't right with the camera, which was set lower than her actual height (he's got a real eye for detail, clearly).
The now-retired Kirsch admits he was working 100-hour weeks during the production of Metroid Prime, and that he would part company with Retro Studios part-way through the development of Metroid Prime 3 as he was suffering from burnout. During his 32-year career, he has worked on World Of Warcraft, Dota 2, Portal, and Quake.