Soy Sauce is Not Named After Soybeans
The existence of both soybeans and soy sauce suggests that humans are aware of two related concepts. Soy sauce is made from soybeans, which makes sense based on common sense, and is the reason it has that name. But when it comes to the origins of words, we cannot make assumptions. The name of soy sauce is unrelated to soybeans. Instead, soy sauce, which claimed the word first, gave soybeans their name.
Despite having Japanese roots, soy sauce has Chinese origins. The Japanese terms for the sauce—soyu or shoyu—come from the Chinese word shi-yu. Does that imply that a soybean is a shoyu bean then? In no way. Known as "daizu" in Japanese, soybeans.
When John Locke wrote about soy sauce, he used the Dutch word saio, which later became soya and eventually soy. The name was reversible because soy sauce was more well known among Dutch and later English speakers than beans were.