...or his arrangements included his body being found before vanishing, to keep people from searching for him. Shisui wasn't some unknown fodder Uchiha. If he just suddenly vanished, people would look for him.
Kabuto just didn't look in the right place.
Kabuto searched everywhere for the bodies of the ninja he brought back. How likely is it that he was able to find people that weren't known until his Edo army, but he "didn't look in the right place" for Shisui? The guy was extremely thorough to the point he found Madara.