My son just bought a unicorn pet for his wizard today and it is having the exact same problem that was described here. He has had a number of different pets in the game, but the only time I've seen this problem is with his new unicorn.
I have found a tempotrary solution for the timid unicorns. Unequip your unicorn, then re-equip it and it should temporarly come out of hiding. Unicorns are shy, timid creatures by nature and tend to hide.
