For one there is no guarantee that the next major upgrade for Traktor will still support non-NI gear, putting the burden of providing correct mappings in the hands of hardware manufacturers and enthusiastic supporters. The first will become less and less inclined to provide mappings as Traktor will not help (supply info) creating them nor help when users experience problems with non-NI controllers and Traktor. So there is a continuity issue, unless you don’t mind having to switch software when your controller is no longer supported.
Secondly, and this is not equally important for every user, NI controllers have bespoke/proprietary jog wheel integration that is ONLY for NI gear. The more important jog wheel response and (lack of) latency is, the better you are off having NI gear.
I have to support Terry_42 in this and say that it pretty much is that simple. Just because you can do something (like use an MC4000 with Traktor) doesn’t mean it’s the best option.
As usual it’s all just our three cents worth and everybody should do what they think will work for them.