shooting at transports

so if I have a squad shooting at a transport, if I make the vehicle explode and the unit transported is now out, can the unit that still has shots to fire still shoot at the unit that was being transported. Or is it that the transport was the only target and the unit must now cease shooting?

All shots are resolved first before any damage results, therefore you don't have guns that have yet to fire, you have dice that you have yet to roll for a vehicle that you now know will blow up because you rolled your damage for the one weapon out of order.

Roll to Hit, Roll for Armor Penetration, Roll for Damage Result. All dice for all weapons, in that order, simultaneously.

Just because you psychically roll the dice before the other dice doesn't mean that those weapons have yet to fire. Strictly speaking you should roll to hit with every gun, then roll for armor penetration before you roll any damage results from any of the guns, fortunately no one around here is a big enough asshole to call you a cheater for not playing the game like a robot but the way you're conducting your shooting phase is misleading you into thinking you're missing out on something that you are not.

Example:

My 5 man tactical squad shoots at an Orc truck. I roll to hit with my melta it hits, I put that dice aside, I roll to hit with my bolters then roll the armor penetration with my melta it pens, I put that aside and roll armor penetration for my bolters...... then after all that I roll for damage results.

If I was shooting at a rhino instead, my squad still fires the bolters but because I want to save time I don't roll any dice for them because my bolter can't glance the armor 11 side I'm shooting at.