How else one can hope to understand better the music of Bach, Buxtehude, Sweelinck, or Scheidemann (just to mention only a few masters from the past)?
Of course there is always harmony and the science of relationships between chords involved but I would say both are always present in a good contrapuntal work, such as a chorale prelude, fugue or ricerar.
Even in the great works of later organ composers, such as Mendelssohn, Franck, Widor, Vierne or Reger we can see plenty of instances of pure horizontal contrapuntal writing.
Counterpoint is indispensible for any person who wants to learn to improvise on the organ. The same could be said about the efforts to compose organ music. Since improvisation is composition at the moment of performance, naturally we can improve our compositional skills just by studying rules of counterpoint.
If you are unsatisfied of your current skills, you would do well to attempt to study counterpoint for two voices (at first). Then you can open up an organ score and see so much more than the bare notes written on the page.
Little by little you would learn to think like a composer, who created such music.
How would it feel for you to have such a skill? How your life would be different, if you could immediately discover the contrapuntal techniques used in the piece you love to play?
Do you think this special knowledge and skill would also impact your performance level? Deep down inside you already know this answer.
By the way, do you want to learn my special powerful techniques which help me to master any piece of organ music up to 10 times faster? If so, download my video Organ Practice Guide.