Another possibility is that the holes are left from the wooden
support bar that runs in front of the pipes to hold them stationary.
Look for screw threads in the holes.  If the pipes were built for
a Seeburg Mortuary Organ with piano, then more than likely they are
not "nodal" pipes.

In instruments with Seeburg-built nodal flute pipes there is some
space between the pipes of, say, 1/2 inch.  If the pipes are close
to the point that they almost touch each other, then they are not
Seeburg nodal pipes but rather are ordinary open flutes pipes.

A nodal pipe (one with a hole about halfway up) in a pipe organ is
generally called "Harmonic Flute" since it plays the second harmonic
at an octave higher pitch than it would without the hole in it.

Don Teach