Basically Microsoft did not officially support 4k sectors in Windows 2008 (even though drives with 4k format seemed to work OK for basic use)
https://support.microsoft.com/en-gb/kb/2510009
Even though the 4K drives appeared to work at a basic level more advanced concepts (relating to VSS, database technologies and/or backups) failed, although in most cases worked if you reformatted to 512e
At the end of the day getting onto Windows 2012 or later at least gets you MS support which should fix VSS (which by the way Backup Exec uses but is not responsible for how it works with 4K) As such against your VSS question you should talk to the vendor of the VSS Provider that has the problem and/or Microsoft to confirm if 4K is an issue.
BE 15 has been tested with some 4K scenarios (you might of course have implemented a scenario we have not tested however if you have a problem we won't deny support if you are on Windows 2012) For BE there may still be some scenarios with limitations against 4K (For instance we may still have a problem with Exchange transaction logs using one sector size against the volume on the Exchange server and a different sector size for your Backup to Disk device for instance - I can't find documentation indicating that this is resolved although we did fix a false identificatiion of this condition that was causing failures where it should have worked.)
