To be perfectly honest, they're not intended for vinyl playback. The phono inputs are primarily for DVS timecode input. I know you're thinking "but what's the difference?" and the answer to that is the quality doesn't need to be as high if it's just for DVS input. All things considered, if you look at what's included on the unit for the cost, they packed a LOT in there. It's not a DJM-quality mixer -- a single 4-channel DJM is more than the cost of the entire DDJ-1000, so obviously there will be places that don't shine as brightly, and in this case, it's the phono inputs.
My recommendation would be to source an external RIAA phono pre-amp and place that between your turntable and the line input.