In determining questions in the United States in Congress assembled each state shall have one vote could a person correctly argue that this quote violates the principle of popular sovereignty

No. The states are themselves models of popular sovereignty. Each of them has a republican form of government. You can't derive nonrepublican government from republican building blocks. The people get to choose the government of the states, and the states then determined the actions of the national government. There's nothing in that process that violates propular sovereignty.