I dont think when the Doctor talks about his sonic not being able to undo a deadlock seal, he is not talking about ones fitted to cars, he is talking about a seal designed to be a defence against a sonic screwdriver, same for Sarah Janes sonic lipstick.
I had assumed that Ianto was talking about the car having both advanced anti theft technology and sonic deadlocks, in a world where Torchwood is being hunted and killed im sure those kids were given some tec by the government agency, which would allow them to steal it.
It can not be a coincidence that the SUV has been stolen only hours before the hub was blown up.
I am sure it was an innocent theft but will leave the team with a chance to get their hands on some of their gear now Torchwood is gone.