I'm currently playing Silent Threat: Reborn for the FSPort and I'm having trouble
with this mission called "Cloak and Dagger".

In this part where you're supposed to scan the cargo freighters and stop any pirate ones from
stealing cargo, I scanned them all and I still have no way of telling which ones are the bad guys.
For all I know I could mistakenly destroy a friendly one so I just keep failing the mission every flipping time.

Are you by chance color blind?

That mission uses purple color for neutral and unidentified targets, green for friendly, red for confirmed hostile ones... if you have trouble telling these colors apart, then indeed you could be having a hard time, since the your biggest clue is that when you scan the pirate freighter it should turn red.

Alternatively you could check your log with F3 and see if your messages give you a hint.

BTW you should post this in the Silent Threat Reborn official forum too, the developers will be glad to help you:

Silent Threat Forum: http://www.hard-light.net/forums/index.php?board=140.0

Freespace and Freespace Open Support Forum: http://www.hard-light.net/forums/index.php?board=151.0