This is also I good question. I bought the WD to see if actually having the rules in my hand would make a different. sadly, it does not. The rule doesn't address the fact that it's an MC with a 360 LoS. in the designers notes section it says you measure from the "muzzle of each gun to the nearest enemy units" - the actual RULE however does not say that. The pod fires at "the nearest enemy unit within range and line of sight" so there isn't a whole lot of ambiguity to me. Are you in LoS and Range? Are you the nearest enemy unit at the end of the shooting phase? Then that's who gets shot.
I do want to point out one key thing in regards to timing - These pods fire at the end of the shooting phase before morale checks are taken - this is important because that means they fire last. You cannot shoot at a transport in hopes of popping it and then having the unit that the pod just deployed mop-up.