Native Stack uses the Android and IOS native navigation systems to navigate between pages.

Native Stack Navigator https://reactnavigation.org/docs/native-stack-navigator/

Stack Navigator https://reactnavigation.org/docs/stack-navigator/

The other one does not really "navigate", but instead will mimick navigation in HTML/JavaScript (SPA essentially). They say they try to make it feel like the native navigation, but it may not exactly be the same or as performant. However, it will be significantly more customizable. You can customize your transitions between pages. With the native approach its gonna be inpractible to impossible to customize a lot of things. What you can customize, you will need to do once for every OS (Android, IOS) unless the navigation library provides a way to customize what you want and deals with OS differences.

Generally when people want to make cross platform apps. Wherever sensible they tend to gravitate towards javascript based solutions. Using native approaches only when absolutely necessary. It´s great that react native gives you the ability to tap into native apis. But using native approaches forces you to also use a physical phone (or emulator) to test those features (properly). Whereas everything that´s web based you can easiely test in your browser, which tends to be much faster for developement speed.