With Shaken, car get checked (as Troy said) for roadworthyness. My father-in-law said he got defected for a-n-y-t-h-i-n-g... windscreen wiper blades, rubber door surrounds, fuel filler caps etc. A typical inspection on a "not very well" kept car could set the owner back 2-300,000 yen in repairs.
This is one of the reasons why you get such cheap used cars in Japan, the owners run the shaken out with a modified and abused car, then sell it just before Shaken is up... at a fraction of the price they bought it for, all because returning it back to standard and/or going through Shaken will cost big bucks.
The other big cost in Japan with owning a car is... parking (if you don't live in a house - Dave you lucky bugger! )