Can an enchantment creature with hexproof be targeted by destroy target enchantment card?
No. Hexproof prevents something from being targeted by opponents' spells and abilities &mdash; that's pretty final. You can't target Archetype of Endurance with Naturalize because you can't target it at all; there's nothing special about enchantment removal.

(If you're thinking hexproof is a creature thing, and we're getting around it by targeting their enchantment-enss instead of their creature-ness, that's not how things work in M:tG. Note also that anything can have hexproof: enchantments, players, or even every permanent you control.)

You get around this by doing things that don't target the creature: Dead Drop, Toxic Deluge, Settle the Wreckage, are examples of the kinds of non-targeting effects you'd use, or a plain old Wrath of God effect. Or kill it in combat.