The solution I came up with a long time ago when I lived in a fairly dodgy area was to make the boot independently lockable from inside the car with a device based on an old tractor clutch. One night I came home to find every car boot on the road open with no barrel in the locks apart from mine where the barrel was loose but the boot still closed.
The car was unreliable enough that I needed to carry a decent set of tools round with me to keep it running - back in my student days.
I also had a car radio that had been carefully doctored to look like it had already been stolen once so that it wasn't worth taking. One thief who got into the car lost 50p from his pocket. Ford locks were never much cop and a piece of bent tin would open them.
All that anything like that can do is discourage the casual snatch thief. Hidden out of sight is about the best you can realistically do.
If your laptop has a Kensington lock point I'd be inclined to fix that to a secure point inside the boot. You might need to fit an eyebolt or similar.
With modern cloud-based stuff even if you keep the data on the hard drive it's not so difficult to recover from a theft these days provided you keep "My Documents" backed up at home.
That's one good reason my my son never locks his car, saves broken windows - seriously. Most modern cars now have reasonably effective immobilisers so it's difficult to drive them away without the key and (usually) its transducer.
Back up your stuff - get an external drive to keep at home - do a regular backup. Save some important stuff to a Cloud server like DropBox or OneDrive.
No point locking the bag to the car. Even if the zip is locked as well, a thief could make a quick slash along the fabric of the zip with a Stanley knife and take the laptop, leaving the bag behind.
I think Martin's right. I was toying with ideas such as a forty quid security box bolted into the boot like a gun safe (brilliant for disputes over the last space in the supermarket car park - you just point at the box and ask "Do ya feel lucky, Punk?) but frankly, if someone has come equipped to pop open all the car boot locks then they'll make short work of that.
Locked in the boot in an ordinary bag is the most reasonable solution for most situations IMO - though I once worked for a company that made it clear their laptop was insured for all other risks - but if you left it anywhere in the car, you paid for it.
What are you trying to protect? The laptop or the data it contains? I keep all my sensitive stuff on a cryptolocker memory stick: if you don't guess the password in ten attempts it wipes the data and there's nothing on the laptop that would get anybody into my bank accounts or emails.
Memory stick in pocket, laptop in the boot. That'll do for me.
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