It's likely the same as English spelling. Just years and years of repeated exposure, and you eventually pick up most of it through osmosis

How does anyone manage to keep allll the words pronunciation and spelling they know is already amazing, craming pronouns on top of that isn't much worse

It is not a problem for native speakers though. These kinds of things are only something you think about if you are learning it as a second language later in life. If you grew up with them you just aborb the information and use it without thinking about it.