solid cargo unloader not recognizing/unloading Cinnabar when never seen before

You need to discover resources to select them in the unloaders. They aren’t discovered if they’re in the cargo bay themselves. You likely already discovered fullerene and iridium. This behavior is a bit silly and cargo bay inclusion should count as discovering IMO.

Note the “Empty Storage” button empties the storage a lot quicker than deconstructing

I might have passed through the fullerene & iridium hexes with a manned rocket. Would that count as "discovering"?

I don't think so. The discovering element thing is kinda weird because a dupe or something that counts like one such as auto sweeper need to physically have access to it first. For example, building a pitcher pump on molten niobium counts even if you have never mopped it in the past. But just passing through a gilded asteroid POI wouldn't count, even if you also collect the free floating resources