Removing the wheels would allow placing them in a shed or garage, which seems like a very effective way to protect them from UV
light. I don't bother, but then I'm due for new tires anyway and have no need to protect the old ones; also, my car tires don't
fall apart over a year or two sitting outside (holding up the car), so it doesn't seem like a big concern to me.
Removing the wheels suggests that the trailer would not be supported on the suspension, but instead on the frame. I think this is fine, as long as the supporting jacks hold the frame reasonably close to the
axle (and presumably behind the
axle, rather than in front, since the other point of support will be at the tongue).
I wouldn't worry about the exposed hubs (either plain hubs or brake drums): I don't think the wheels provide meaningful protection for them anyway. I would rather leave them open to get wet and dry with the weather than to enclose them in plastic and risk trapping water.