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)

Not FOSS but free - ReadEra, it's working extremely well. No ads or anything, the only feature the paid version has is cloud sync of your library, and sync reading progress across devices.

Been using it for 8 years or so, bought it at some point just because it works without a hitch since basically forever.

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.

If you use Linux Foalite would be the besbest choice