No it will not hurt anything.
Quick lesson in “wire science” when wires that are laid next to each other transfer date/electricity they get “cross talk” actually it creates a electro-magnetic field. This will create errors in data transfer.
So they inserted a “dummy” wire that was just grounded out. This neutral wire would buffer out cross talk by absorbing the noise.
Here is an exerpt from www.HowStuffWorks.com
http://www.howstuffworks.com/ide2.htm
Ultra DMA increased the DMA transfer rate from ATA-2’s 16.67 MB/sec to 33.33 MB/sec. In addition to the existing cable that uses 40 pins and 40 conductors (wires), this version introduces a cable that has 80 conductors. The other 40 conductors are ground wires interspersed between the standard 40 conductors to improve signal quality. ATA-4 is also known as Ultra DMA, Ultra ATA and Ultra ATA/33.
ATA-5: The major update in ATA-5 is auto detection of which cable is used: the 40-conductor or 80-conductor version. Ultra DMA is increased to 66.67 MB/sec with the use of the 80-conductor cable. ATA-5 is also called Ultra ATA/66.
So in short: No it won’t hurt anything, if anything it could improve performance. But I doubt it.
