In Okular (for desktop), you can set keyboard shortcuts for various color inversion/shifting modes. Or you can permanently set one in the Accessibility settings.
I use Okular and sometimes Zathura, both can do that through hotkeys (you can also add a button to the toolbar in Okular)
Evince (the standard GNOME pdf reader) has night mode that you can toggle with “Ctrl + i” by default.
Librera on Fdroid will, but it’s a bit unpredictable. It works well enough most of the time
Sioyek also does this
Highly recommend, esp. if you like using vim keybinds (you abviously don’t have to, but IMO it’s a fantastic feature)