All model years are the same, save for colors and decals.
Being a brand-new 2009 model that was built three years ago wouldn't bother me.
I would, however, ask that the battery be tested to ensure it's still good since the battery comes pre-charged, and the longer it sits around, the greater the chance of it going kaput.
What would get my attention is if the bike had obviously been ridden and then sat around with fuel in the tank and fuel system.
Back in the day, I bought a brand-new 1983 Yamaha XT-550K in 1986.
I also bought a brand-new 1986 Yamaha BW-200ES in 1989 or 1990, and a brand-new 1987 Yamaha BW-350T a few months later.
No trouble, and the bikes never skipped a beat.