Commvault tried to blame my AUX copy chunk errors on a fragmented magnetic library when I first started using the software almost 3 years ago. I figure it this way - you never have to take a primary storage array "offline" to defrag it, so this didn't quite cut it with me. Granted, most storage vendors have a defrag or scrub utility but, quite frankly, I've had little to no success with windows defrag or any other 3rd party product. Now I'm talking about 2 TB volumes, not a few gigs or even a few hundred gigs. With just little activity on my volumes, I let defrag run for days and days and it never finished. In the end Commvault released a patch that fixed it like I knew they would - just have to beat it out of them at times. Now to answer your question - there is no harm in defragging a magnetic library, but is there a specific reason to? I've seen no speed or throughput degradation to my backup storage arrays that can be attributed to fragmentation. With all of the read/writes as a result of backups and aux copies, even if I could defrag it would do little to no good I think.
Hope this helps.