Cortez thinks I'm gay, will it affect my chances to date women?

Solution 1:

When you go to the club with Cortez, he will mention that he's "checking out the eyecandy". After he says this, you have two dialog options:

"I'm eyecandy too" or "The eyecandy on stage is good enough for me".

Choosing the second one will let him know that you're not gay, without hurting his feelings, and you'll stay good friends, which will allow you to pursue other interests.

Solution 2:

No. Cortez thinking you're interested in him will have no effect on your chances of romancing the other potential candidates (except Traynor since she bats for the home team).

Like the previous titles, you will reach a point where you tell your potential suitor that you just aren't into them like that. With Cortez, that time is, ironically enough, when you go have drinks with him at Purgatory.