They do, and Tamagotchi even has its own app. The problem is that phones are filled with all kinds of other shit that demand your attention too, from videos to emails and even other game apps. The pet calling for food and bathing on your phone doesn't mean so much when you can just delete the app when you get annoyed with it.
A physical virtual pet is far more immediate and intimate. You make the conscious decision to start one and carry it around, to pull it out of your pocket and care for it when it needs you. It's a feeling a phone application just can't replicate. And that's even before mentioning the shell designs, which are just really nice and make the Tamas pleasant to look at and carry around.