ippon, nihon, and ippiki, nihiki are numbers with counter units added (different from hitori, futari). Counter units exist in English. It's common to say "I have 600 head of cattle" vs "I have 600 cattle". "600 head of cattle" is exactly the same in Japanese, "牛600頭". The counters in Japanese are also often similar to the way we use the words in English. You don't say "I have 12 wines". You say "I have 12 bottles of wine". "12 bottles of wine" is very similar to "ワイン12本”. I think "5 loaves of bread" also fits. You'd never say "I have 5 breads". You have to say "I have 5 loaves of bread"
I get there's a subtle difference but it's not that far off. We also say "I have 6 meters of rope". "meters" is the counting unit, which is the same concept as all the Japanese counting units.
As for the onomatopoeias, at some point you get used to them and they feel like they fit and you can start to pick them up without having them explained. Even the ones that don't seem like the make a sound, start to make a sound, at least in my mind once I've internalized it.
Not the same but in some sense similar, dogs don't say "bark" but with enough repetition many people perceive "bark" instead of the actual sound the small dog is making.