Are auras permanents MTG?

Auras are indeed permanent cards. The only card types that do not count as permanent cards are instant and sorcery.

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Then, does darksteel mutation change creature type?

It also won't overwrite the effect of counters. The enchanted creature will be only an artifact and a creature, not any other card types. It will be only an Insect, not any other creature types. Thereof, how does indestructible work in mtg? Indestructible is a common keyword in MTG. Magic: The Gathering rule 702.12 states a permanent with Indestructible can't be destroyed and "such permanent aren't destroyed by lethal damage, and they ignore the state-based action that checks for lethal damage."

Keeping this in consideration, can you put two enchantments on a creature?

You can have any number of Enchantments attached to a given Creature, unless the cards themselves say otherwise. Is an enchantment a permanent? An enchantment is a permanent. See rule 303, "Enchantments." See also Aura. 303.1. A player who has priority may cast an enchantment card from their hand during a main phase of their turn when the stack is empty.

What does Hexproof protect against?

Hexproof is an evergreen keyword ability that prevents a permanent or player from being the target of spells or abilities played by opponents.