[KTibow]

It's unfortunate that this isn't a default option. The only viewer I've seen that happens to be able to do this is Gnome's Document Viewer.

[johnisgood]

You can invert colors in MuPDF, and someone added a way to save your settings (incl. width and height, position of window, inverted color, zoom) and whatnot upon quitting. This person added a search history too (per PDF). I forgot who though, which might make my comment not-so-helpful.

If interested, I am willing to look for it, might be someone I follow.

[salutis]

Also PDF Tools for Emacs, where PDF can match your theme.