Why would sand need numbers to exist? I can pile up sand without ever knowing how many grains of sand are in the piles. I can not see how combining several things requires numbers, it only requires several things, i.e. you have to define what the different things are, where the boundaries between them are.
you can count apples instead of sand
Obviously, that was just an example. You need several objects.
yet physical phenomena, such as the formation of sand or apples, depends on quantity
It does only insofar as you need several distinct objects, it does not depend on numbers. Also note that you have to arbitrarily decide to count apples or grains of sand. Why apples or grains, why not atoms or quarks? There is a bunch of stuff and you have to divide into several distinct objects before you can even start to count them. The fact that you decide to divide all the quarks and electrons into things you call apples is an arbitrary decision and imposes a structure on top of the things that are there by itself. Only with this imposed structure and your [imagined] action of dividing and combining subsets of the things does something like counting, and numbers and addition emerge.
a hadron with three quarks is a baryon, a hadron with a different number is fundamentally different
Arbitrary definition. There are quarks, calling collections of them baryons or mesons or tetraquarks is an arbitrary definition made by humans, albeit a useful one.