I think it's cited occasionally by justices like Clarence Thomas, but it seems only when he's in the minority advocating something that most people see as being inline with his Catholicism under the guise of natural law.
Has a majority opinion ever taken in to account the natural moral law (please see encyclopedic definition) that is at odds, circumvents or makes up for lapses in the constitution? Has it ever been used to interpret the constitution?
I did not find any instance in which the US Supreme Court has ever used "Natural Moral Law." However, it did use "Moral Law" 13 times.
It has used "Natural Law" 83 times. The most recent in 1996 in Seminole Tribe of Florida v. Florida, 517 U.S. 44 (1996).
It has been used to interpret the constitution
In DISTRICT OF COLUMBIA ET AL. v. HELLER the SCOTUS decided that the right to bear arms was an individual right and not a collective right limited to organised militias, and that the Second Amendment to the Constitution merely codified that existing individual right (rather than creating the right).
William Blackstone in Vol. 1, Commentaries on the Laws of England (1765) states:
The fifth and last auxiliary right of the subject, that I shall at present mention, is that of having arms for their defense, suitable to their condition and degree, and such as are allowed by law. Which is also declared by the same statute I W. & M. st.2. c. 2. and is indeed a public allowance, under due restrictions, of the natural right of resistance and self-preservation, when the sanctions of society and laws are found insufficient to restrain the violence of oppression.
SCOTUS refer to this saying:
By the time of the founding, the right to have arms had become fundamental for English subjects. See Malcolm 122–134. Blackstone, whose works, we have said, “constituted the preeminent authority on English law for the founding generation,” Alden v. Maine, 527 U. S. 706, 715 (1999), cited the arms provision of the Bill of Rights as one of the fundamental rights of Englishmen. See 1 Blackstone 136, 139–140 (1765). His description of it cannot possibly be thought to tie it to militia or military service. It was, he said, “the natural right of resistance and selfpreservation,” id., at 139, and “the right of having and using arms for self-preservation and defence,” id., at 140; Cite as: 554 U. S. ____ (2008) 21 Opinion of the Court see also 3 id., at 2–4 (1768). Other contemporary authorities concurred.
The rationale appears to be that because the right of resistance and self-preservation is a natural right it cannot be a right conditional on military service.
The SCOTUS majority opinion concludes:
Putting all of these textual elements together, we find that they guarantee the individual right to possess and carry weapons in case of confrontation. This meaning is strongly confirmed by the historical background of the Second Amendment. We look to this because it has always been widely understood that the Second Amendment, like the First and Fourth Amendments, codified a pre-existing right. The very text of the Second Amendment implicitly recognizes the pre-existence of the right and declares only that it “shall not be infringed.” As we said in United States v. Cruikshank, 92 U. S. 542, 553 (1876), “[t]his is not a right granted by the Constitution. Neither is it in any manner dependent upon that instrument for its existence. The Second amendment declares that it shall not be infringed
