Justin,
I can't speak to the effectiveness of the configuration you describe, but I can tell you what we're running here. We have BudTool running on a Sun (Solaris-2.6/SPARC), with the Sun controlling the robotics, and with three of the four tape drives connected to the Sun. The third tape drive is connected to our NetApp.
BudTool loads the appropriate tape into the NetApp's drive, and then uses NDMP to tell the NetApp to back itself up to its locally-attached DLT7k. At the same time, it can tell pretty much any Unix machine, or any NetApp or other NDMP speaker to send its backup data back to the BudTool server (Sun) over the network. It all works here just fine. We even have the Intelliguard (Legato) NDMP server for WinNT on some of our NT systems, and back those guys up over the network to the jukebox, as well.
Whether it's best to ask the NetApp to control the jukebox, or connect some of the tape drives to the Sun BudTool server, will depend on your preference. Personally, I'd hate to suck up CPU and network bandwidth on a filer just to backup some Unix or even other NetApp systems, unless I had no choice. Keep in mind that licensing costs may play a part in your decision here, too. But BudTool should allow you to plug things together in many ways.
It remains to be seen whether a future NDMP-speaking Legato NetWorker will work as flexibly as BudTool does in our configuration.
Regards,