Getting ready to deploy a 3TB to be used as shared backup and file storage for Windows 7/10 and Linux. I know I need to set it to GPT partition table, but what I'd the best cluster/allocation unit size? 4k is default but I know 1k and 2k would support this size volume... Is there any reason not to use a smaller allocation unit size to make more efficient use of disk space with smaller files or is better to stick the default 4k size for some reason?
It really depends on the files you plan to store on that 3 TB HDD. However, it's highly recommended to use the default 4K for any NTFS hard drive that is smaller than 16 TB.
Just like @whs mentioned, smaller allocation unit size would make sense only if you're keeping small doc files (for example) This way a very small portion of the HDD space will be wasted. If you plan to back up massive data like HD videos, photos, movies, etc., then even bigger than the 4K default AUS would be better.
I'd suggest you to read through this article about the Allocation Unit Size Differences
Good luck. Hope this helps. :)