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The most obvious benefit that I'm aware of is that neutered horses train a game year longer before leveling off (not continuing to add points to their score when trained). Therefore, if you neuter them after they've leveled off, they stop adding points to their show scores without that additional game year of training benefits.

I've definitely noticed this with ordinary foundations. Intact foundations level off when they turn 10. Neutered foundations level level off when they turn 11. I haven't kept track of exceptional and exceptionally perfect producers.

All horses, whether neutered or intact, continue to add points to your showing bonus as long as they don't get stuck placing at the very bottom of their classes. Inconsistency does affect their placement in classes, so very inconsistent horses will have a lot of variation in where they place.