I'm glad to see this has sparked so much discussion!
I firmly believe that both type 1 and typ2 diabetes would still be an issue in New Eden. Type 2 diabetes results from poor dietary habits, obesity, and other lifestyle factors. All three of those are probably an issue within the Federation more than anywhere else, thanks to their focus on personal liberties and pleasure. Keep in mind Quafe is a VERY popular sugar drink, Karsoth was morbidly obese, and with the proliferation of drones and automation people would be less likely to do hard labor themselves.
Type 1 diabetes is genetic in nature, IIRC. Unless the Federation has been practicing eugenics (or the Terrans before them), it would likely still be around. Since we have no evidence to suggest such an assumption, we should default to thinking it's still around.