Once the destiny deck get to 50% in stack size, one card from each stack is added to the deck and is reshuffled again.

The destiny deck is generated by taking 2 cards from each of the 5 stacks (6 if using treachery) and when a crisis card requires 2 are placed into the middle.

this allows players to card count the brown,red and blue card plays easily as they are the most scarce.

By adding in further replenishment to the deck it is now possible to prevent card counting and moreover fill the deck with treachery at the most inopportune time (which is almost always bad). Making for a more desperate early game.

I'm not sure how you can count cards with the destiny deck. You have no way of knowing which cards came from the destiny deck and which cards were contributed by a player. That's the whole reason you shuffle the stack of skill cards before revealing them.