You can't destroy face-down monsters with Makiu because the monster that would be destroyed by it have requirement. Face down monster's ATK, DEF, Attribute and Type is unknown until it flipped face-up. So it won't be affected by card's effect that spesifically requires monster stats (ATK, DEF, Attribute, Type, Name).
If the card's effect only says destroy without any spesific requirements for monster stats (ex: Dark Hole), then it would/could destroy face down monster too.
However, you still can tribute face-down monster as a cost to activate card like Crush Card Virus, Spiritual Water Art - Aoi, etc.