This is a topic that was already well-covered in The Physics of Superheroes. But while The Atom and Ant-Man/Giant-Man/Too-Many-Names-Man have size changing as their explicit super power, a lot of anime (and near-anime) characters do it incidentally, as a part of other transformations. Of course, so does the Hulk.
For example, Devilman is considerably taller as the demon Amon than as the human Akira. (Or in Mazinger Z vs. Devilman, much taller.) Well, at least he’s supernatural.
When Pokemon evolve, they change instantly from one form to the other, including an instant increase (or occasionally decrease) in size.
In GaoGaiGar, when a human becomes a Zonder, they get bigger even before combining with any machines, and shrink back down when purified. And among the robot/vehicle transformations, some, particularly Volfogg, have the same sort of issues as Transformers; the transformation makes physical sense otherwise, except for the fact that the robot and the car aren’t the same size.
And speaking of transforming robots…
Gold Lightan, from the series of the same name, is a building-sized robot who shrinks down to become a cigarette lighter.
And then there’s Dragon Ball, where the light of the full moon makes Goku change from his normal size to an Oozaru, a King Kong-sized giant monkey. (Usually referred to in English as a Great Ape, presumably because in both real life and fiction most apes are larger than most monkeys, but it has a tail and otherwise looks more like a monkey than an ape. Of course, the term “great ape” is also a real-life term; orangutans, chimpanzees, and gorillas are great apes.)
Here we see Goku as an adult next to the Great Ape form of Gohan.
All of these have the same basic issue. Where does the extra mass come from or go? In most cases these transformations don’t show any other sign of involving the vast amounts of energy it would take to account for it by energy/mass conversion (remember, E=mc2, and c is the speed of light, a very large number). And if they actually violate conservation of energy, they have other issues.