Background: The Act of May 24, 1934 repealed the Naturalization Act of 1855, which had provided that a person born outside the United States is a US citizen at birth if their father, at the time of their birth, was a US citizen who had resided in the US (at any prior point in time). The Act of 1934 allowed US citizen mothers to pass down their citizenship in the same way as US citizen fathers, but wasn't retroactive. The Act of 1994 corrected that omission, making it as if the Act of 1934 had been retroactive.
While we're unlikely to see a person born before May 24, 1934 run for president, if this issue did come up, there is a way for the Supreme Court to sidestep the issue of the interpretation of the natural-born citizen clause. In Sessions v. Morales-Santana (2017), the Supreme Court ruled that it was unconstitutional to require US citizen fathers to have spent 10 years of physical presence in the US in order to transmit citizenship to their children born abroad, while only requiring 1 year of continuous residency for unwed US citizen mothers. The basis for the ruling was the Fifth Amendment, which since the 1970s or so has been held to prohibit discrimination on the basis of sex by the federal government. Note that Morales-Santana did not overrule Nguyen v. INS (2001), but in Nguyen, the Court justified the requirements of §1409(a)(4) by reference to the biological reality that a mother is present at her child's birth while a father might not be. In Morales-Santana no convincing justification for disparate treatment based on gender was presented, and it seems similarly unlikely that one could be produced for the Act of 1855, under which it was impossible for a US citizen mother to transmit citizenship. If the Court decided that the Act of 1855 violated the Fifth Amendment, then it could decide that the people given citizenship by the Act of 1994 really had been natural-born citizens under the Act of 1855 anyway, and thus eligible for the presidency. I think this is the most likely way for the Court to rule.
(I believe the courts are only allowed to consider the Fifth Amendment argument if it's actually raised in the district court. Most likely, anyone going to court to argue that they're qualified for the presidency—whether it's suing an election official who refuses to put them on the ballot, or being sued by one of their opponents—would raise both arguments: that they are a natural-born citizen under both the Act of 1855 and the Act of 1994.)
The courts could be forced to confront the issue of the interpretation of the natural-born citizen clause directly in a case involving §1409(a), which appears to operate by granting citizenship retroactively to birth as soon as the conditions of paragraphs (3) and (4) are met, provided that the child is still under 18 at that time. See related question. In that case I have no idea how the Supreme Court would rule. One option that the Court would have at its disposal is to try to distinguish between a statute that's enacted before the person's birth and one that's enacted after. The latter case more strongly implicates the founders' concerns about foreign influence over the United States, since an influential figure might be able to convince Congress to pass a private bill giving them the ability to run for president.