Why Odin has virtually indestructible durability while Thor "only" has superhuman (by the Official Marvel Handbook)?

Because Odin is far more powerful than Thor.

Durability is the physical resistance of the character, not how much powerful he is. I've never seen Odin withstand the gravity of a neutron star, or get tanked by the Destroyer... Or is it possible he has virtually indestructible durability because the numerous return from death without any aid?

That much power can easily be used for defence, Odin doesn't have as many actual feats because he is very rarely the centre of attention for a comic.

Because Odin has the sky-falter empowerment. When Thor is the king of asgard he's a lot stronger.

Odin has taken hits from the likes of Thanos, the Silver Surfer and other powerful foes without moving and unhurt. Thor has not. Therefore Odin is tougher.