Virginia, in their acceptance of the Constitution, made it explicitly clear that they withheld the right to withdraw from that Union...and here is the relevant phrase—”We the Delegates of the People of Virginia....declare and make known that the powers granted under the Constitution being derived from the People of the United States may be resumed by them whensoever the same shall be perverted to their injury or oppression and that every power not granted thereby remains with them and at their will.” New York and Rhode Island also had clauses that allowed secession...Since all these states ratification of the Constitution was considered valid, then the clauses where they secured that right to secession was also valid—and due to the equal protection clause, what was valid for one state would also be equally valid for another.
Those signing statements were all very nice - but none of them hold the force of law superior to federal law.
You can't pencil in your own reservations to a contract that the other parties have already signed and expect them to be regarded as valid. If you could, you could insert clauses that nullified the whole document you are signing.
The "equal protection clause" usual refers to the 14th Amendment which was only ratified after the Civil War. There was also the "privileges and immunities" clause of Article IV, but that doesn't really apply here either.
Actually the relevant phrase is this: "We the said Delegates, in the name and in behalf of the people of Virginia, do by these presents assent to, and ratify the Constitution recommended on the seventeenth day of September, one thousand seven hundred and eighty seven, by the Federal Convention for the Government of the United States; hereby announcing to all those whom it may concern, that the said Constitution is binding upon the said People, according to an authentic copy hereto annexed..."
Which means that regardless of what else they said in their ratification document, they agreed to abide by and be bound by the Constitution itself. And if their act of secession was unconstitutional then it was also invalid.