The two-crew rule is not actually an official regulation in the US as far as I know; it is simply a near-universal company policy. There has been considerable debate over whether it’s something that ought to be regulated, with US authorities apparently content with the current situation. In Europe, some airlines moved to the two-crew rules after the Germanwings crash, but they actually went back on it within a couple years as regulatory authorities complained that it increased the time that the door was open (and consequently hijacking risk). I don’t buy that argument but I’m also not 100% convinced that a regulatory solution is needed.
Regardless, the NTSB did not appear to consider it at all in its report, either because the risk of pilot suicide was seen as too low to be a major concern, or because US airlines had already taken action voluntarily. Keep in mind that at that time, EgyptAir 990 was the only major disaster caused by pilot suicide; the only previous cases that I know of are an attempted suicide by a Japan Airlines pilot and a successful one on a commuter flight in Morocco. It was the Germanwings crash that was really the wakeup call, based on what I know about the subject.