Because I've suffered the results of trying to stream data over pipes with AutoNegotiate on each end and different vendors invoved (in my case Bay Switches and Compaq NICs)
Regular network traffic was acceptable, if a little on the slow side, but BackupExec was getting between 1.5 and 3.0 MB/min That's right MegaBytes per minute, not Megabits per sec. Hardsetting both ends cleared that up.
You SHOULD be OK if you hardset your switch ports and leave the NICs in Auto. If you move your servers around enough for both ends hardset to cause problems, you are moving them around way too much.
I've been offering this advice to people with slow network backups for years and no one has ever said that it made no difference, while many report significant speed ups