Frankly put by the Summer of 1945 the Home Islands were blasted ruins for the most part. For over a year they had been worked over by massive B-29 raids, the carrier task force had come in close and worked over targets of opportunity, and even the battleships and cruisers had come into range and blasted coastal targets with gunfire.

What AA Batteries were still operational, and more importantly had ammo, were concentrated around Tokyo and the Palace, and the expected invasion areas. While the majority of the air force was being held in reserve to challenge the invasion in large part as either full on suicide missions or tacitly one way trips.

Occasionally small flights would be sent to bombers operating alone or that were thought to be damaged, but they also had to deal with the not insubstantial defensive armament, persistent Allied fighter sweeps, and the reality that B-29's could fly essentially as fast as they could and just about at their max altitude, dragging out daylight interceptions. And in desperation outright ramming attacks were an accepted tactic.

So no there was no stealth involved or even attempt to hide that lone and small groups of B-29's were over the target cities, because it was already a common occurrence, to take photos or monitor weather, and defenses were in such a shambles that it was considered acceptable by Allied commanders to fly like that. Especially when other much more massive raids are going on continuously.

This thread from a year ago has some good stuff on the topic: https://www.reddit.com/r/AskHistorians/comments/35rwix/how_were_single_unescorted_bombers_able_to/