Well, there are TWO reasons you might want "short" trade routes.
1) Close Borders implies they don't like you much. Trade means they do (I've averted wars via trade)
2) Many economic starbases can make it very, very, very profitable
In my current game, I expanded like mad and ended up colonizing the same star system as a neighboring empire. Trade has, so far, averted complete war. Oh, there's been a couple of minor skirmishes, but nothing that a few hundred BC bribe won't solve. Its expensive, but business is business.