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Sending 3 cards from the top of your Deck to the Graveyard is part of the effect of “Destruction of Destiny”. It is not a cost.
If “Macro Cosmos” is on the field the 3 cards will be removed from play, but you will still take damage for any Spell or Trap Cards.
You cannot activate “Destruction of Destiny” if you have less than 3 cards in your Deck.
All the damage is dealt in a single sum. So if you send 3 Spell or Trap Cards you take 3000 damage, not 1000 damage three times.