I actually have some interesting new information to report regarding that. Turns out that there are unpackers for the .PAK files used in Metroid Prime 1 and 2 on the Gamecube (apparently the files were encoded differently for each game). If Prime 3 had as much of its content ported to the Wii as I suspect, one of the unpackers might work on its files.
This doesn't mean the game uses MDL0s. In fact, it probably doesn't because it wasn't made in Japan and wasn't originally a Wii game. But the only way to know with 100% certainty is to unpack those files. (I did not find the MDL0 string when I looked at them with a hex editor, but the compression could have affected that.)