The probability of encountering eggs contaminated
inside with salmonella is actually very very low. In the US, according to one industry association (which I admit might be biased), 1 in 20,000 or 0.005%. If we assume that Japan is even safer, then obviously an even lower probability.
However, the outside shell of the egg can be contaminated with all sorts of shit and other crap harboring bacteria other than salmonella. The ones that you see in the supermarket have been cleaned - unless you were naive enough to believe that they came out of the hen all white and pristine.
For using serving raw eggs where the diners break their own eggs (eg. let's say for
sukiyaki), I was taught to disinfect the shells in a warm bath of vinegar and salt -- and then rinsed and dried - before presentation. Here is a quick explanation:
How to Easily Clean and Disinfect Fresh Eggs | eHow.com