Saying $H_2O$ is 64 fundamental particles is largely right.
One trivial problem is that sometimes the oxygen is another stable isotope like $^{17}O$ or $^{18}O$ with 1 or 2 extra neutrons, adding 3 or 6 quarks.
A more profound issue is that when quarks are bound into hadrons they do not exist as neat separate particles but as components in a complex mess of virtual quarks and gluons. Now, one can say that virtual particles are not real and should not be counted: they are just a mathematical contrivance to describe the behaviour of the actually real thing, the quantum fields. But in a sense real elementary particles are also mere excitations of the fields. One could say there are no particles at all and just a handful of fields extending across the universe, but this is likely not a useful answer to the question.
As always, the answer to the question depends a bit on what it is supposed to do. In some applications protons and neutrons count as fundamental particles, in others quarks.