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 is an illegal target by the time Maelstrom Pulse tries to resolve, the spell won't resolve. You won't destroy any permanents at all. If the target is legal but not destroyed (most likely because it has indestructible), you do destroy other permanents with the same name.

Unless a token is a copy of another permanent or was explicitly given a name by the effect that created it, its name is the subtypes it was given when it was created plus the word "Token." For example, if an effect creates a 1/1 Soldier creature token, that token is named "Soldier Token."