First, each country (or group of countries, sometimes) sets its own rules for security. While they more or less align because they generally follow the same objective, there is no obligation for them to be the same everywhere. Japan and the US can have different rules, and you can't do anything about that.
Next, rules are not always applied consistently and extensively. They are human, they miss things. Frequent travellers have lots of stories of the forgotten Swiss Army knife or screwdriver somewhere in their bag which went through a dozen flights and as many security checks in different countries before someone finally noticed it and confiscated it (for an item that is nearly universally banned). Different scanner technologies may also have an influence, as well as training.
In this specific case, there may also be a cultural aspect: a Japanese agent is more likely to recognise a samurai sword handle than a US agent.