The evidence is in things like Autocarpus Viriles which affect growth on all colonies. Hover over the growth display on the planet screen and you will see the bonus from Autocarpus Viriles and you will see it change with multiple copies. The same is true for Snuggler Colonies, Monsatium Deposits, and probably others I can't think of at the moment.
By the end of the game, I will own all of the Autocarpus Viriles in the Galaxy, either by purchase or conquest, but that is only one of my obsessions.