[jesselt]

I'm not sure what you mean by "not all of them know all of Kanji." If they're native Japanese, they should know pretty much all of the Kanji that are in use. There are some that are no longer in use (though I expect most people would know a lot of those anyways.)

There is something like 2500-3000 in use iirc (I don't know where 5000 came from, I've never heard of that many outside of Chinese) and if you want to be fluent you should understand all of them. There are thousands upon thousands of compounds that you also need to know (which also frequently change the pronunciation.)

You would have to take like 15 years of Japanese courses to learn them all if you didn't do any outside study. In other words, Japanese courses aren't going to teach you all of the Kanji - They should teach you quite a few of them with compounds, but there just really isn't enough time to teach all of them.

It's also not really correct to say that Hiragana is the 'main' writing form - Kanji are used when writing almost as frequently as possible. Katakana is also very common. It would be correct to say that all three combined are their main writing system.