That's a old problem for me : I link Illustrator / Photoshop files in Indesign, and these files can also have various links to various files. When I do a "package" in Indesign, it copies the links but not the links of links, and that often cause problems.
Can you make all the softwares capable of recursively package sub-links, and also check for doubles (because various links sometimes have links to the same sub-files).