As a judge at UIL I heard groups where the director had modified the instrumentation for various reasons to improve the performance. I didn't see any notes in the score. I have done the same sort of modifications without notes in the score and had no comments from the judges.
However, one year in Honor Band competition I modified my March with written permission from the publisher/copyright holder and didn't add notes to the score. The area judges caught my changes and it was suggested I add the authorization letter to the scores for state level. For legal purposes I recommend getting publisher permission for any major changes.