In regards to the Cards vs The rules.  

THE CARD

The card says have an encounter with the yellow player in his or her home system  However if you are the yellow player either: A) Have an encounter with any other player in your home system or B) discard this card and draw again.

THE RULES

Even though a player may not have ships on thier home planet that player must still defend it.

If the yellow player has 5 planets and thier system and only has colonies on three of them  and i draw the yellow card. Can I attack one of the planets without colonies since it is still there planet?

If i am the yellow player and i draw this card and i only have 2 planets, the other three are colonized can i setup a colony on one of those planets without having an encounter with another player. Like if the planet had nobody on it.

I have asked people on other forums about this. they have said that they can attack the uncolonized planets. What do you guys think.

Tank said:

Yes. You can choose any planet in Yellow's system, and yellow will be the defense regardless of who does or does not have ships on that planet.

Tank said:

No. If there are any players on your home planet, you must choose one of them to be the defense. Any others are bystanders.

To add to Bill's reponse:  if you draw your own color in destiny, and one of your home planets is COMPLETELY empty of ships, you may just land on it, and call it a successful encounter.