I want to find out about something. Is his effect a designating effect?

No, he's effect does not target.

Legendary Jujitsu Master is not a targeting effect as you have NO choice in what gets bounced back to the top of the Deck. Anything that attacks it while it is in Defense Position will get sent back to the top of the owner's Deck.

"Except" monsters that destroy it while face-down, like Ssauke Samurai and Mystic Swordsman L2/4/6.

Of course. Always exceptions to such rules (most of the time).