I don't think it was really a secret. The Emperor in Kyoto was in charge of religous affairs and so had a certain amount of power, but the Shogun in Edo was the reason that you'd see representatives from every province travelling across the realm to pay respects and leave hostages (sankin-kotai) in alternating years. There was a whole system of roads constructed across Japan for this purpose (the Tokaido and Nakasendo being the most famous), with inns all along the routes for the groups to stop. They didn't have to leave hostages with the emperor.

Specifically to you question, the mother of Tokugawa Tsunayoshi was a commoner, but was able to provide him valuable political advice (it was an unusual situation - most kids were taken away from their mothers at the age of 5, but his father wanted him to be more feminine as he was not the original heir). I don't recall reading anything about her that would indicate she had a false idea about the Emperor actually running things. Likewise, when peasants revolted after a volcanic eruption and their lord was unreasonable, they marched toward Edo to petition the shogun, not to Kyoto to petition the emperor. (Source: Bodart-Bailey The Dog Shogun)