I'm having the same problem, which I thought I nearly solved. There are a whole host of things that I'm working on for my company. Firstly, upgrading and migrating their moodle. Secondly, making it highly available. Their moodledata dir is 40GB+ so it's not trivial just to move around.
I've got an NFS server that hosts the moodledata dir abd the webserver can mount in a second - that's great. However, SCORM content isn't working well with it (which is what I'm still working on). We are using the repository plugin to allow us to use course content directly from the file-system, instead of uploading them manually.
I'm still researching this issue and am happy to share what I've done so far, as it is quite complex and difficult to document here.