Hello! Political scientist here, not a historian, but my educational background deals pretty heavily with the American Constitution.

The 9th Amendment was very cleverly written by James Madison to satisfy Federalists who despised the idea of a list of rights because they viewed it as both unnecessary and counterproductive. Alexander Hamilton wrote in Federalist #84 that it is unnecessary because the body of the Constitution doesn't specifically allow Congress to pass laws that restrict certain rights. The example that he uses is the liberty of the press:

For why declare that things shall not be done which there is no power to do? Why, for instance, should it be said that the liberty of the press shall not be restrained, when no power is given by which restrictions may be imposed?

On the issue of its counter-productivity, it could be argued that a hypothetical government would view a list of rights as implying that those are the exclusive rights of the people and that any other right that wasn't specifically listed could be infringed upon.

Now, to more directly answer your question we can look back at the Fifth Amendment, which uses a very particular phrase "[no person shall] be deprived of life, liberty, or property, without due process of law; nor shall private property be taken for public use, without just compensation." The concept of life, liberty, and property is something developed from John Locke's Second Treatise of Government where he argues that people are born with inherent rights and some governments choose to respect those rights, rather than rights being something that governments grant to its populace. So it's clear that the Fifth and Ninth (and later the Due Process Clause in the Fourteenth) were written in order to protect rights that were not specifically enumerated in the Bill of Rights, and that they were heavily influenced by Lockean principles.

Locke himself wrote extensively on "inalienable rights" that every person is born with; he reasoned that every person has a basic right to preserve their own life, make their own choices so long as they don't interfere with the lives of other people, and to believe the way they choose to do so. This, I think, is the answer to your question. This amendment was really written to uphold the principles of the Constitution and of the classical liberal ideology, and not really specific individual rights, otherwise there would have been another amendment protecting some other right that the framers could have thought up.

In practical application, the Ninth Amendment has had little attention by the Supreme Court, however the vague mentions of life, liberty, and property in the Due Process Clauses of Fifth and Fourteenth Amendments have received considerable discussion by creating a principle known as substantive due process where the Supreme Court takes up the task of deciding which rights it wants to deem "fundamental." These rights are then given the same protection (strict scrutiny) as the rights specifically enumerated in the Bill of Rights. These include the right to marriage (Loving v. Virginia), the right to privacy (Union Pacific R. Co. v. Botsford), the right of self defense, and for a time, the right of contract (Lochner v. New York), among others.