Hi I have my ten in bits at the moment, yearly strip/ repair/clean/lube rebuild.
I had wondered about that parts function as well, it just appears to be a loom end as it is capped, so does not plug any where, perhaps yamaha added it for some future spec, maybe god forbid EGR. http://en.wikipedia.org/wiki/Exhaust_gas_recirculation

my advise is secure it with cable ties so it cannot rub and forget