Question: As a role player, what do I see as actually happening to my impounded assets? Are there NPC ships flying about that gather them up and move them, even in W-space? Is there some sort of hyperspace transport system that has my assets stuffed into it, and they cannot be popped out for awhile? Or what?

If I dock a super in a citadel, and that citadel is destroyed, the super then enters purgatory until xfered to another XL Citadel within the same system.

Unfortunately, there will not always be a 2nd XL citadel in the same system (and if there is it will likely be under assault). And since we lost the fight, we won't be building a 2nd citadel to xfer supers to. This means I will not be able to access my super at all, which is really bad.

So I'd never log off with a super docked in a citadel.

We need another option, such as the super being delivered to a safe spot in the same system rather than a citadel.

Let's say a Nyx is moored at a structure, allowing the pilot to enjoy the use of ships other than a space coffin. An opposing alliance attacks and manages to destroy the structure before the owner can return to it. Instead of giving away such a valuable prize and the owner losing everything, the Nyx activates an automated security system*.
On destruction of the attached structure the ship automatically overcharges and activates its jump drive (ignoring any nearby bubbles), vanishes to a safe location and cloaks up. Of course finding a safe location and re-establishing contact with the proper owner is risky, and may take time (likely several days). In order to board the ship again the owner has to wait a random period, then perform some kind of mini-quest to locate his auto-piloted hull.
Once found, there would be a short vulnerability period (2-3mins) as the vessel repairs and re-calibrates itself from the emergency jump. Once this is successfully completed, the ship can be used again as normal.

This introduces a small element of risk to losing structures, without the all-or-nothing aspect for people with ~100bn isk hulls. The attacker denies the owner use of a powerful ship for a period of time, and has an opportunity to kill it if they pay very careful attention to the area later. The owner has a decent chance to get their ship back in the event of a disaster, especially if they have friends to help recover it.

Edit: the same mechanic can be used against corp thefts. If a mooring structure is tampered with for whatever reason (perhaps the owning corp wants to pull it down, perhaps someone is misusing their roles), the ship activates its security system in the same way. This gives some peace of mind for the owner.

*if affordable cars can have security systems to prevent theft, why can't futuristic space flagships?