You're right, 5111 is more pertinent here.
5111(a)(1) says “shall mint and issue coins” but qualifies it explicitly with “in amounts the Secretary decides are necessary to meet the needs of the United States”. This is a clear delegation of authority.
If you don't think zero pennies is a permissible amount, what about one penny? Two? What minimum number are you arguing for here, and what's your justification for it?
If Congress had wanted to set a minimum number, they could have done so.
Reading it as ”shall mint” is wrong, I think. “Shall” qualifies the whole clause “mint in amounts the Secretary decides (etc.)”.
Understood that way, 5111 makes it unlawful to mint any pennies if the Secretary decides that none are necessary.