I'm a regular international flyer, my hand luggage is always scanned, and despite my best efforts it often gets searched, either due to mistakes on my part, or security being extra cautious. On my most recent flight I estimate about 5-10% of my fellow passengers also had their hand luggage opened and searched by hand.
On the other hand, I have never had any issues with checked in luggage, I've never been pulled to one side and asked to explain anything, and as far as I can tell my luggage has never been searched (unless someone has picked the lock and then been very tidy in re-packing it)
So, my guess is that either 1) checked-in luggage isn't scanned as well as hand luggage, or 2) checked-in luggage is scanned by some super-hi-tech scanners that are infallible in identifying suspicious devices and never need checking by a person.
If the answer is option 1) then why doesn't checked-in luggage need such a thorough check? What's stopping a bad-guy putting a couple of kilos of something dodgy into his bag that brings down the aircraft over the Atlantic?
If the answer is option 2) then why can't the infallible super-hi-tech scanners be used on hand luggage too so no-one ever needs to be pulled over for a manual search?