That's becasue each of them must be overlayed over a group (or groups). It's just the way Metroid Prime does things I suppose. It might be because the models mainly all use 256x256 sized texture, combing all the textures for a particular object might result in a really large image size, so they minimize size by having smaller, but more textures.
SSBM also does this, but to an even greater extent. A typical character model from MP has about 8 groups, using about 14 textures (which includes shaders, specular maps, etc), while in smash bros, the trophie Young Link has 52 groups, using 39 textures.
Lol and that's not the best example you posted, because I only see 3 textures, not 40 ; )