I don't know how well that fits how gravity works in Spelljammer, but I am somewhat amused by the idea of D&D spacefarers hypothesizing the existence of an intangible, undetectable object at a system's barycenter because they don't understand physics.
Physics barely has any connection with Spelljammer. Any object over 1 ton in mass creates a 1g gravity plane along its longest axis. Most planets are large enough to have gravity that points down at all points, but some planets can be disks or other shapes with gravity that actually follows a gravity planes.
So the most likely answer to a missing object at a barycenter is magic, which is common to spacefarers.