Customs in Japan is quite slow with all the foreigners, especially Asians visiting there. During my visit last month I was on the customs line for 45 minutes and there were 14 custom agents! I'd say 90% of the visitors were Asian.
Baggage check was really quick. No lines. In the last 22 visits there these past 16 years, I have never been asked to open my bags, nor was I searched. However it does depend on what country you are coming from and how you are dressed. For example, I've mostly seen westerners with long hair and beards being searched more often than not. This is due to the fact that if you look like a rocker, or hip-hopper, they think that you probably do drugs. Also, young Japanese returning from the Phillipines or Thailand are more likely to be searched also. The baggage checkers will usually ask you one or two questions while looking directly into your eyes before checking your baggage or waving you through.
Also, one word of caution: Do NOT even think of carrying so much as joint or any other drug as if they catch you, you will be immediately be transported to jail for at least a week or more and will not even be able to make so much as a phone call.