Yes the other is a Yorkie named Bob and Naomi has both dogs because at the time of their breakup Heath had 5 films ahead of him and felt he couldn't be the "daddy" they deserved as he would be gone so much. Naomi had fewer projects and travelling to handle at the time. Also, Bob is a very sickly little guy that has had to be raised on babyfood due to a birth defect that affect his intestines and Naomi had more time to be with him and help him through these things.
As Matilda grows older I wouldn't be at all surprised to see kitties and dogs showing up at the Ledger household at any time. He's quite the animal lover.
Theresa