Although Nintendo was not involved in developing the actual Nintendo games on CD-i, they did have certain requirements to meet the quality and look & feel of their characters. Most of the times the easy way to get around this was using the same type of sprites and graphics that Nintendo was using, like in Super Mario's Wacky Worlds. That was more or less a pure copy of what Nintendo did in Super Mario World for the Super Nintendo.
When Philips created the boxart of Hotel Mario, they made use of original Nintendo resources. Mario is a recreated copy of the cover in the japanese Super Mario Bros (and was used in the european version of Super Mario Bros 2, see below.
Even Animation Magic's Link and Zelda titles made use of original Nintendo art. This was taken from the timeline of Link to the Past that was also used in Japan.
The reason why we have Nintendo games on CD-i is because Nintendo wanted to use Philips technology (and patents) in new SNES CD hardware. They even asked Philips to develop it (purely a money issue). Nintendo eventually cancelled the deal because they wanted more control over their own properties, but they were still eager to use certain Philips patents in videogame technology (Philips had lots of those because of their rich history in the Magnavox Oddyssey and the MSX standard. As a gentlemen-agreement, Philips allowed Nintendo to use CD technology patents and Nintendo allowed Philips to use their IP in a number of CD-i software projects.
Link in Link: Faces of Evil is a recreation of Link as how he was positioned on the back cover of the japanese version of The Legend of Zelda: A Link to the Past for the SNES. Zelda in Zelda: Wand of Gamelon is as well based on Zelda how she is drawn on that same japanese cover, made by the same artist.
Philips chose to recreate the Mario character as close as possible as this boxart reference. While the games itself were developed outside of Nintendo, the boxarts of at least Hotel Mario, Link: Faces of Evil and Zelda: Wand of Gamelon were actually approved by Nintendo.
[Source in contact by Interactive Dreams]
