I just picked up Edge of Empire. I noticed a lot of the career specializations make things class skills that are already class skills per the base career. I don't understand why this is the case, and if it's explained in the book I missed it. What effect does this have?

It allows you to take a second free rank in the skill as one of the two free ranks for it being your initial Spec.

You get one free rank from four of your Career skills and one free rank from two of your Specialisation's skills.

If you choose the same skill from both, you could start a skill at rank 2 without spending any XP.

Also, the duplication is there due to the fact that specs are open to everyone. The skills associated with each spec are the ones deemed most important to them. Thus when a character takes that spec those skills become career skills unless already career skills. Thus when a Hired Gun/Marauder takes the Assassin spec, he will gain those skills as career skills, but no ranks as in character creation.