If you would like to balance the load using multiple HBA ports, the approach you mention is a good way to do it. I usually try to do the SAN zoning so that each drive is zoned to particular HBA port.
This approach was easier back when tape drives only had one FC port. Today a lot of tape drives supports load-balancing over multiple paths. But to my knowledge NBU does not implement load-balancing, but I stand corrected if that is the case.
Based on the assumption that NBU does not use load-balancing, then NBU would just select the first available path to the tape drive, and it is quite possible that it selects paths to multiple tape drives on the same host HBA port, meaning all I/O goes through the same port. And this way you would not balance the load of multiple HBA ports on the media server.
Therefore I usually still go for selectively zone the paths, so we can "steer" NBU somewhat.
I'm not sure what you mean when you say you had problems, but if you change the configuration, and get missing paths in device configuration, you should just delete all tape drives first, and then run a new scan in the wizard. New paths will be created in NBU this way, and you should be able to access all tape drives.
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