Congress certainly has the power to change Acts of Congress. It could very well have been that they revised the Act of 1790 because the description they had placed in it did not match what their original intent was and wanted to remove/correct their mistake. They may have come to the conclusion that Congress did not have the authority to re-define the term natural born citizen without an amendment process and thus removed it from the Act.
My point is that you cannot look at just the 1790 Act for guidance on this issue. Both Acts and the change made in reference to the term natural born citizen to just citizen together tell us something very important.
It's convincing evidence of what they thought it meant, and, therefore, how the Constitution should be interpreted. It shoots down de Vattel, etc. SCOTUS frequently engages in such lines of reasoning.
The fact that the 1795 act does not use the term NBC does not mean they were contradicting the 1790 act with respect to NBC. They could easily have written "citizen, but shall not be deemed to be natural born." But they did not. And, even if they had, they don't get to change their mind about the meaning of the Constitution without going through the amendment process.