Drill files from Kicad for PTH and NPTH
In KiCad, in the dialog for generating drill files, there is a checkbox "Merge PTH and NPTH holes into one file."

As others have said, it may be only certain fabs (e.g. OSHPark) that require at most one drill file.

Another gotcha is that in the KiCad footprint, in the pad for a NPTH hole, you must insure that the size of the pad is same size as the drill size.  (KiCad won't let you specify "None" for copper layers.)  Otherwise, 1) KiCad generates copper under and surrounding the hole in the Gerbers, and 2) the fab algorithms will see a thin ring of copper around the hole, and proceed to plate the hole, despite that the type of the pad in KiCad is "NPTH".