A face-down creature has no name, so it doesn't have the same name as anything else.
Maelstrom Pulse has only one target. Other permanents with the same name will be destroyed even if they have hexproof or protection.
If the target permanent becomes an illegal target for Maelstrom Pulse, the spell doesn't resolve. Nothing is destroyed.
The name of a creature token is the same as the creature types it was created with unless the token is a copy of another creature or the effect that created the token specifically gives it a different name. For example, a 1/1 red Elemental creature token created by Young Pyromancer and a 4/4 green Elemental creature token created by Walker of the Grove are both named "Elemental."
If Maelstrom Pulse resolves but the target permanent isn't destroyed (perhaps because it regenerates or has indestructible), all other permanents with the same name as it will still be destroyed.