The Vigilante did have a short life later as a recon bird, but never saw one up close.
As you noted, the Viggie had a unique linear bomb bay from which the nuclear “shape” could be ejected while the pilot flew various maneuvers. During the initial trials the equipment & ejection methods were not reliable - the bomb bay was never used as such in the fleet. One unconfirmed story was that whenever the test pilot executed a certain release maneuver the shape followed the flight path of the aircraft almost exactly, forcing the pilot to do an unplanned maneuver to “shake the shape”.
It's career as a bomber basically over before it really began the Vigilante ended up as a very capable recce platform from about 1964 until the end of the 1970s. The sensors were state of the art, and replacing the Viggie’s package with the TARPS pod for the F14 was considered by many in the recce community as a step backwards.
IIRC the plane had the dubious distinction of having the highest combat loss-to-total aircraft deployed ratio of the Vietnam War. This was due to the mission profile and the relatively small number of aircraft involved, not the performance of the aircraft/crews themselves. Those post-strike assessment missions were brutal...
In the end, the Viggie was removed from service due to its large size (& carrier deck multiple) and high maintenance cost. The big problem towards the end was a lack of tail hooks - North American was willing to restart a production line, but it was cost prohibitive. On the last deployments the aircraft spent as much time as possible shore based to save wear & tear on the hooks.
Squirting out the nuke aft had major problems, no bomb was ever dropped that way. The main problem with the plane was that its high landing speed and other flight characteristics made is really hard to land on a carrier...even in the best of conditions...bad weather or nighttime operations would have been very dicey..The main reason the Navy dropped the plane was the rapid development of missiles launched from subs..