Responding to MMD 020110, concerning holes drilled in flute pipes:

The most likely reason is that the pipes are "harmonic" flutes,
meaning that the pipe is designed to sound an octave above the otherwise
expected pitch (for that length).  This was very common in early 20th
century organs.  The hole will be found almost exactly at one-half the
speaking length.  If the hole is covered,  the sound will be an octave
lower than designed (if it will sound at all).

Another possibility:  If the hole is drilled in the lower portion (the
"foot" of the pipe), it may represent a stop-gap measure to prevent the
pipe from "partially ciphering" if there is a leak in the pipe's valve.
This is more often found in reed pipes than in flue pipes.

Bill Flynt