To play it all out: why the heck is Nick Locarno flying around in a little ship capable of disabling the systems on larger warships, transporting(?) the ships and crews to some planet while leaving wreckage behind?

He’s not. He’s making deals with the lower deckers of those ships to make it look like his ship can do all that. They say in the episode that the lower deckers of the kidnapped crews are disabling the shields and weapons. Then he makes off with the crews and some of their technology for reasons yet unknown.