This just happened on my first run through with Chokepoint. Shinobi Assassin came up in the environment then Stripped Resources promptly destroyed it. I have one text saying, "Destroy all environment cards. Put any targets destroyed this way face-down in the villain play area."
But another text states, "When this card would be destroyed, move it to the top of a hero deck instead."
I would tend to think that the Shinobi Assassin would go to the top of a hero deck.
Then Resurrection Ritual came up, but I didn't have to make any choices there. But I could see a potential fuzziness there as well.
I'm hoping Parse's Gauge Power allows the Shinobi to be moved to the bottom of the deck. It does not say "Reveal" or any of the words used on the card. It says "look at".