In the USA, it certainly makes at least a minor difference. There is a running theme on Jalopnik of stories like this
They apparently couldn't start it. I had to tell him four different
times to push in the clutch, because it's a standard transmission.
My first thought was I guess we don't have driver's ed in school
anymore because no one knows how to drive a stick. And my second thing
was, don't shoot me because you can't start the car. I'm trying to
help you out here. You know. Thankfully they didn't.
Obviously not scientific, as it is only one of many stories like this. But even if only a handful of thieves can not drive stick that is at least a tiny bit safer for American manuals.
It is not a single event either, maybe not common but it does happen somewhat frequently and here is another example
Swahn says one of them pulled out a gun, got in the car, and tried to
take off. Deputies say neither of them knew how to drive a car with a
manual transmission. They got out and fled on foot.
Also, this story has been reused dozens of times, Carinsurance.com, MSN, and here is FOX
The best information I can see is anecdotal from the police force:
800,000 vehicles were reported stolen in the U.S., one every 40
seconds), but police say that only a tiny percentage of stolen cars
have manual transmissions.
So maybe that "tiny fraction" means %.001 or ~5% inline with the manual sales.
I think the best we can do for an answer though is either it depends or it is unknown:
Frank Scafidi, director of public affairs for the National Insurance
Crime Bureau, which tracks car-theft trends, says he's not aware of
any data to support or refute that idea.
Read more: http://www.foxbusiness.com/personal-finance/2011/03/28/stick-shift-anti-theft-device/#ixzz2SdCjZyrl