The 16th Amendment did not override the Supreme Court decision.
The 16th Amendment removed the founder's wise protection against direct taxation. The 16th Amendment removed the provision to levy taxes in proportion to the population.
I know that the income tax is supposed to be an indirect tax
The Income Tax is and is supposed to be a direct tax. The 16th Amendment removed the provision in Article 1. Section 9. calling for “No Capitation, or other direct, Tax shall be laid, unless in Proportion to the Census or Enumeration herein before directed to be taken”.
Article XVI. The Congress shall have power to lay and collect taxes on incomes, from whatever source derived, without apportionment among the several States, and without regard to any census or enumeration.
The easiest way to explain is that prior to the 16th Amendment if the government wanted to incur a $50 million expenditure they would tax the state’s $50 Million. If the population were 50 Million then the tax would be $1 each paid by the state. A truly remarkable system of taxation. Imagine today when the Congress is noodleing over $300 Billion program knowing that each citizen would be paying $1000. I think a lot more thought would go into the spending than it does now.