Article II, Section 2 of the Constitution rerquires two thirds of the Senators PRESENT to ratify a treaty. There was never any Senate vote on a treaty annexing Hawai'i that received two-thirds of THOSE PRESENT as required by the Constitution.  In your example, the total vote in the Senate was 63 votes.  Your 42 was 2/3 of those VOTING, not present.

The U.S. government at the time did not contest that the treaty submitted to the Senate never passed.  The President withdrew the proposed treaties when it became clear ratification lacked the votes.  They did not play games with the constitutional requirements for ratification.  Instead, the Congress passed a joint resolution "annexing" the Kingdom.  A joint resolution is nothing more than an internal document, otherwise any country could pass a resolution seizing any other country.

There is no "executive agreement" between the United States and the Kingdom ratifying in any way the seizure of the Kingdom by the United States.