Q1: If userA logs in to my site via Joomla, and userB logs in to Facebook directly using the same computer, does JFBC automatically thinks that userA and userB are the same person if userA is registered in my site with a different email address from the email address that the userB has with FB?
No. The user would have to click the "Login with Facebook" button and intentionally associate the account in some way. If the emails are different and the user hasn't taken an action, JFBConnect will assume they are different.
Q2: If the answer to Q1 is NO, and if userA and userB in the above scenario are in fact the same person (even though two different email addresses are used with my site and with fb), is there a way to ask JFBConnect to recognize that fact so the fb friends of userB can be visible to userA?
Not unless the user has a) approved your Facebook Application and b) associated that account with JFBConnect (and therefore Joomla). Without that, JFBConnect tries to make as little assumptions as possible about who userB may be for privacy and security issues.
I hope that helps answer your questions,
Alex