My theory is Joey can't afford Pokeballs.... His money goes to everybody he fights.... He and Rattata survive on berries he grows.... But it's ok because his berries are like the top percentage of berries.... In fact he sells them to pay for battles, phone bills and HP ups....
Sounds like a reasonable theory. Maybe he also gets some berries from Bug Catcher Wade in Route 31.
Of course.... They run the berry business between Violet and Cherrygrove.... They had to pay protect to Team Rocket.... But you changed that and now they run the whole damn berry scene from Sinnoh down to Hoenn....