I made the 3 pipes on the right, each one in a collection, and then instanced the collections to create the 3 pipes on the left. It renders fine but, for some reason, in the viewport, I see the boole objects that cut out the holes in the original 3 pipe collections:
…in viewport… in this case hiding just hides the original object but not the instances and disable completly disables (and so also not showing ) for every instance…
Side note: you need one more pipe, organ registers are in sets of octaves (and your heights aren’t quite right for an octave), I’d suggest some reference. The organ in Westminster Abbey and the Temple Square organ in Salt Lake City are both very famous and widely photographed