Kalapas are defined as the smallest units of physical matter If we stop at wikipedia, then Hinduism, modern physics and the ancient greeks have a theory of the atom. But a definition does not really equate to a theory.
Kalapas are material units very much smaller than atoms, which die out immediately after they come into being. Each kalapa is a mass formed of the eight basic constituents of matter, the solid, liquid, calorific and oscillatory, together with color, smell, taste, and nutriment.
Essentials of Buddhism
Note the two fundamental characteristics of Kalapas - (1) they are transitory/ephemeral and (2) they have 8 types which are useful for meditation, but not for physics.
Meditation on kalapas seems sound and instructive; reasoning based on kalapas seems to be a misuse. The Buddha was trying to free people from reality; not to advance technology.
As a thought experiment, imagine that I define the smallest unit of matter as the foo. Have I created an atomic theory similar to that of the ancient Greeks? No - I've just relabled something. It isn't a theory until I offer testable predictions about the interaction of foo particles.
@Rajib says it clearly and succinctly:
The Indian theories are philosophical and metaphysical, not scientific. While they do describe the infinite and the infinitesimal, the descriptions are not meant to be quantifiable. Being descriptive, they cannot be the bases of scientific inquiry.
That is a better answer than mine.