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.

Evince (the standard GNOME pdf reader) has night mode that you can toggle with “Ctrl + i” by default.

Librera can read PDF - there’s also a dark mode. The app isn’t the best looking, and the controls are unconventional, but you’ll get used to it.

Zathura lets you theme your pdf files.