While the main Office apps remain traditional desktop Windows applications, Microsoft has been developing a modern version of OneNote using the Universal Windows Platform (UWP) APIs for some years; it's arguably one of the more complex and capable UWP applications available today.
In Office 2019 shipping later this year, that new version of OneNote is moving to the foreground and will become the primary version of OneNote. The existing desktop application, OneNote 2016, will continue to be supported in maintenance mode, receiving bug fixes through October 2020 and security fixes until October 2025. But new features are going to be reserved for UWP version.
Microsoft has already said that Office 2019 will require Windows 10—it's the only version of Windows still in mainstream support—so the switch to using a UWP app should be fairly transparent. Clean installations of Office 2019 won't include OneNote 2016 som standard, but if it's already there, it won't be harmed by upgrading.
Right now, there are some features found in the desktop app not present in the UWP; Microsoft is working to fill in the gaps, with features such as tags and Class Notebook support coming later this year. The company is also working on a new sync engine that provides near-instantaneous updates across Windows, Mac, iOS, Android, and the Web.