I believe we have seen it done in many games where Nintendo and many other game companies have referenced there past or many other things or points from history in the naming of a location, this is often referred to as an easter egg and works in a similar way to some of the cat faces that have appeared in the backdrops of Nintendo's games over the years. The interesting point that can be made in Pikmin 3 is the naming of the home planet that the games protagonist Alph, Brittany and Charlie come from. the name Koppai which is the home planet is actually an interesting reference to Nintendo's past, when the company was founded in 1889 it was originally named Nintendo Koppai. Obviously they pulled this past reference into play as a nice name for the home planet in Pikmin 3 and because they liked the name, not to mention it sounds like a good name for an Alien planet.
Another little bit of trivia that is seen in Pikmin 3 is the naming of PNF 404. While it has ben proven that this name fits in with how NASA names unimportant planets it is also believed that this is actually a pun. 404 is an HTML error code and PNF stands for Page Not Found when you are having trouble finding a page on the internet. Which in itself is quite interesting, so there you have it to interesting bits of trivia from Pikmin 3.