Depends what each bike costs. If the bikes are of the same price-ish then I would go for the 1000 as it has a few extra bits chassis-wise.
OTOH, it's very easy to extract more power from an 800ss with very little outlay. My mildly tweaked road example knocks out 82bhp at the rear wheel, will stay with a friends 996 til 140mph and has been clocked by others at 150mph. It would take a good 1000 to leave that.
The 800 motor is very sweet and free-revving.
Be aware that the 800 spec varies wildly.
800 wiki here:
http://en.wikipedia.org/wiki/Ducati_800SS
Threaded Mode