But that's just the point, instead of using a new word for atoms when sub particles were discovered, the existing meaning was set aside.
This reminds me of how the prefixes we use in computing hardware aren't right either. Your PC might have 8 gigabytes of RAM, but it doesn't literally have 8,000 megabytes or 8 billion bytes, and the same problem with mega- and kilo- too. Somehow we manage and when we're talking gigawatts giga means 10^9, and when we're talking gigabytes in computing we know it has a special meaning, 2^30.
Same prefix, two different usages depending on context. The only thing I can promise you though is we're never going to adopt gibi, mebi and kibi, at least not in my lifetime anyway.
Understanding the history and evolution can be interesting or informative as to why things are the way they are. So yeah, one upon a time "sub-atomic" would make no sense, it makes sense not of course. We're familiar and used to the idea. Wasn't always the case though.
atoms are made of protons neutrons and electrons each which is made of 3 quantoms.
The analogy is quite apt, really, just switching out bigness in place of smallness.
Electrons are currently thought to be indivisible, and protons and neutrons are made of three quarks each.
I've never heard of the word "quantom" before... where does it come from?