OnyX is the main application. The Maintenance and Deeper applications are parts of OnyX. Thus, if you use OnyX, the Maintenance and the Deeper applications are redundant!
All the applications are signed and notarized.
OnyX is a multifunction utility for macOS that you can use to verify the startup disk and the structure of its system files, to run tasks of cleaning and computer maintenance, to configure some hidden parameters of many Apple applications, and more.
Maintenance is an operating system maintenance and cleaning utility for macOS that you can use to perform miscellaneous tasks of computer maintenance: run periodic scripts; rebuild the databases; delete application, font, and system caches; and more.
Deeper is a personalization utility for macOS that you can use to enable and disable the hidden functions of the Finder, Dock, Safari, iTunes/Music, login window, and many Apple applications, and more.