With many objects directly, the file size can become unnecessary and the scene is polluted with many individual (often little) objects/materials which must be managed somehow.
Linking groups is the clean way to bring an asset into the scene (one that strictly doesn't need/want further editing/changes).
I think I know what the problem is...I have not saved all my assets whilst Indigo addon was installed, this means they don't have "indigo_mesh" information.
A solution would be to have fallback indigo_mesh settings if this information is not available.