Official comment
An answer from the product teams, and it's pretty much what I expected:
The DJM-450 is designed more for privately used whereas DJM-900NXS2 is for professional use, as such, the circuit configuration and the parts used in DJM-450 and DJM-900NXS2, including the phono pre-amps, are different.The product team focussed exclusively on audio quality in all processes when designing and manufacturing the DJM-900NXS2, and because of that, the quality of not just the phono but all the inputs and outputs within the DJM-900NXS2 are superior than those of DJM-450. The audio quality of the DJM-450 still meets our high standards for a product of this price range, but when compared to the DJM-900NSX2, the more expensive mixer will clearly have better components and sound.