They very much understood their situation. That was the means of control. Their incomes were directly defined by agricultural productivity, and their expenses largely controlled by the shogun. Daimyo couldn't meaningfully communicate with each other, easily intermarry, or form alliances. They were forced to maintain huge retinues and lavish estates, and the shogun could bankrupt them or kill their family at any point.

The shogunate needed to do some balancing along the way (including the introduction of metallic currency), but the government had enough levers to keep the samurai in line, right up until they couldn't.