Great game, but a couple of newbie questions

[Jones]

This my first SE game, and I think its great.Very addictive.However,the manual doesn't really do a very good job of explaining all of the little details to the game. So I've got a couple of newbie questions, and I hope they don't sound too dumb.
1. Does it matter what you title a ship or colony when you first create it? The reason I ask is because I wasn't creating any "military bases". I was calling any planet with a shipyard a "construction base", any planet with high resource values either "mining,farming,or refining", and anything else either "research or intelligence bases". Well into the game, I created a colony and accidently called it a military base. The next turn I got a message saying my population in that system was happier because of the increased military presence. So that got me thinking these titles that I thought didn't really affect the game may really do something.

2. What does "counter intelligence" do? It takes a long time to complete, and I've always gotten a message saying it's failed. Am I doing something wrong?

Thanks for any replies, and I apologize for any typos. )