The secret missions have been transformed in DMC2 to secret rooms. These are rooms that can only be accessed by pressing circle when next to the doorways. You will be transported to a square room, and forced to fight two waves of enemies. As you uncover more secret rooms, the enemies get harder. The reward for completing these missions is extra red orbs, a white orb, and sometimes a blue orb fragment.

You can go through the same doorways in Hard mode, and in Dante/Lucia must Die mode to gain more secret rooms. I know that Dante has 20 and Lucia has 10 per difficulty mode.

Dante
mission 1 - 1
mission 2 - 2
mission 3 - 1
mission 4 - 2
mission 5 - 3
mission 6 - 0
mission 7 - 1
mission 8 - 0
mission 9 - 0
mission 10 - 1
mission 11 - 2
mission 12 - 2
mission 13 - 0
mission 14 - 1
mission 15 - 0
mission 16 - 1
mission 17 - 0
mission 18 - 0

Lucia
Mission 1 - 2
Mission 2 - 0
Mission 3 - 2
Mission 4 - 0
Mission 5 - 1
Mission 6 - 0
Mission 7 - 1
Mission 8 - 1
Mission 9 - 0
Mission 10 - 0
Mission 11 - 0
Mission 12 - 1
Mission 13 - 0