Rural children hired to work on farms get less money. The urban ones earn money, though.
It doesn't matter whether you use 'though' or 'however'. The main problems are logical.
1. "The urban ones earn money, though" only makes sense if the rural children don't earn
any.
2. The rural children earn less money than whom? If the answer is "the urban ones", then it's obvious that the "urban ones earn money, though".
This should be one consistent sentence.
"Rural children hired to work on farms get less money than urban children." This could still be ambiguous if the urban children are not working on farms.