The set of permanents affected by Heroic Intervention is determined as the spell resolves. Permanents you begin to control later in the turn won't gain hexproof and indestructible.

A planeswalker with indestructible still loses loyalty counters as it's dealt damage and will still be put into its owner's graveyard if its loyalty reaches 0.

A battle with indestructible still loses defense counters as it's dealt damage. If it's a Siege, it will still be exiled when the last defense counter is removed from it, and its controller may still cast it transformed without paying its mana cost.