Not only are pretty much all contemporary philosophers attentive to this fact, but there's an active philosophical literature about the naturalness of some terms as opposed to others, and about how one can reasonably distinguish natural kinds from non-natural ones. Particularly interesting is some of the recent work in metaphilosophy and in particular metametaphysics, which examines whether (or when) ontological disputes are substantive, what is the function of philosophical disputes, when one can be justified in believing a metaphysical doctrine, etc. (Note: This field is not merely awesome because it has a hilarious name.)

Don't confuse disagreements about which natural kinds exist, and hence about which disputes are substantive, with disagreements about whether there's a distinction between substantive and non-substantive disputes at all.