Moodle doesn't inject or modify any of the SCORM files. SCORM packages have to be unzipped before being served to the browser.
Moodle stores file path/structure information in the database rather than on the file system (for all files - not just SCORM) - If you have the same file/scorm in multiple courses it only stores one copy "on disk" - decreasing the amount of files stored on disk, but this design also enables Moodle to take advantage of cheaper cloud storage solutions like Amazons S3/Object storage - there should be a few similar posts in the forums if you search generically for where files are stored by Moodle.
Moodle stores file path/structure information in the database rather than on the file system (for all files - not just SCORM) - If you have the same file/scorm in multiple courses it only stores one copy "on disk" - decreasing the amount of files stored on disk, but this design also enables Moodle to take advantage of cheaper cloud storage solutions like Amazons S3/Object storage - there should be a few similar posts in the forums if you search generically for where files are stored by Moodle.