The JTV line may be on the way out, but I doubt that Variax is. if they were going to EOL Variax itself, L6 wouldn't have just introduced the 'Standard', or put a Variax port on the (brand-new) Helix. I would guess/hope that it means Yamaha will build some nice mid-to-high end Variaxes.
This may just be wishful thinking: I have an HD-25 and a Helix, and am holding back on the Variax, hoping for a new version. If they don't announce something at NAMM, I may have to give in and go through the dusty JTV-69s at Sweetwater until I get a good one :) .