There are a range of different ways to link SCORM packages to a SCORM module in Moodle.. but If you upgrade to Moodle 2 then it will only store one version of the zip on disk (and possibly only one copy of the extracted zip but I haven't checked this) - the interface will show aliases to the same file held on disk.
You can also locate your zip package oustide your course folder - either directly on your server or within somewhere like the site files area and then provide the url to that zip inside each course. If using Moodle 1.9 each course will have to extract the zip into it's own course area so that may not quite be enough.
The other option is to create a directory on your moodle webserver that's in the wwwroot and has all the scorm packages extracted in a folder - then inside the SCORM module use a url that links to the extracted imsmanifest.xml file - for this to work the folder must be publicly accessible and on the same url as your moodle site - so this means if someone knows that url they can download your SCORM packages without having to login.
The best option is to use Moodle 2 as it just does this behind the scenes.