Since animal's size is encoded in a few genes that are specifically marked to evolve very quickly, any ill effects (for non-extreme settings) would be extremely unlikely. Besides, mutations in those genes exist without manipulation too, you have small tigers, and you have large cats. Those animals don't go crazy, so ...
Even in humans you have everything. From people who grow 2-3 centimeters from when they are born, to people who grow to 2.5 meters. While most examples have a somewhat short lifespan, it's not drastically short. Even though our skeleton clearly has problems with anything over 2 meters.
And you do see that happening. There are a lot of species that have changed size in documented history. The trend seems to be that anything that lives in cities, from tigers to rats, evolves to the size of a large cat, which seems to be optimal for survival. Also their colors change to very dark patterns that are bloody hard to see in the dark (and they only come out in the dark in cities). In nature there is more variation, but as habitats have generally become smaller, animals have shrunk too.
(these are neither ponys nor foals, they're fully grown adult horses, no if you're not a baby you can't ride them. They come in sizes varying from 30cm to 120cm. You also have horse races that have a "port"height (meaning their shoulders) of 2m)
Actually there'd be a tremendous market for perpetual puppies and kittens. Even if their life span is a little on the short side.