Its definitely tough for sure but you have to remember Shonen Jump is just one of many shonen manga outlets and beyond that there are more genres and probably hundreds of monthly/weekly magazines. Do they pay the same? No. Its the same as anywhere. A lot of people either work in the background either on the publication side or the production side as assistants or they have their own serialized manga with a magazine not as widely known as SJ. There are a lot of people being regularly published who maintain day jobs. This is coming from having known people who worked in the manga industry either as assistants or people I know whose works are serialized in monthly manga magazines.
Lets not forget the absolutely HUGE culture of self publishing in Japan with Comiket being the biggest indie comics fest in the world.
And of course the industry has changed because of the way we can now just share our stuff online without having to go through gatekeepers. That applies to Japan as well.
Comics are a tough industry wherever you go. But there are always sneaky little side channels if you have the desire to make them. But more than likely you shouldnât put all of your eggs in one basket.