For Clarity - In Star Citizen:
IR - passive tracking seeker that looks at the target's heat signature. Real life example is the AIM-9 Sidewinder family.
Cross-section - the size of the target from the angle the sensor sees it. In game it's supposed to be active radar but can also be optical. Real life example would be AMRAAM, Sparrow or Hellfire.
EM - passive sensor that sniffs out and homes in on the electrical signals and noise made by the target. Real life example is the HARM anti-radar missile.
Its been a few patches since I did any extensive testing, and ship's EM/IR values have shifted significantly since then. But I've noticed that IR tends to stay higher than EM, which can be readily changed by what systems are powered up and in use.
More practically - I rarely use missiles in the PU as the cost adds up quickly. In AC, there is a kind of gentlemen's agreement not to use missiles in the PvP section. Or at least their used to be. The Rattlesnakes (multiple-head IR) were very popular for a long time, but I'm not sure that any flavor holds sway right now.