I mark proper nouns as known. Shame on me. The thought behind that is that it is of some value to know that a word is a name. It usually is of very low value though and it differs from word to word really. If I´m learning French it is of good value to know that Germany is “Allemagne” and London is “Londres” and of some value to know that “François” is a masculine name and “Françoise” is a feminine name and that neither of these words means “French” as a language.
But it really isn´t of much use to your French to know that “John” is a masculine name if you already speak English, or to know the name of a place where the name is the same in French as in some other language you know (“Toronto” for example). It also isn´t of great use to see some names that are right out of languages you don´t know at all and simply realize they are names of people, for example: " The African Union is facing a backlash after terminating the appointment of Arikana Chihombori-Quao, its ambassador to the United States " - I´m going to get that Chihombori-Quao is a name and mark it as “known”, but I´m not going to remember the word or recognize it if I see it in it´s native language. The words that make up a name might even have a specific meaning in it´s native language, for all I know this name could mean “brave-runner” or “honest-merchant”, which I wouldn´t know and then again the words don´t belong to the language I´m learning anyway.
Optimally one should really differentiate between proper nouns like I´ve mentioned in the first paragraph and the ones like in the second paragraph. Mark most or all of the first kind as known and none of the others. It´s just too much of a bother to me. It would slow me down and also change the way I´ve been doing to so far. It does skew my word count, but in the end the word count is a flawed measure no matter what, as others have pointed out already. I see it as something that correlates with how many words I know and how much and diverse reading I´ve done, rather than directly measuring any of these things. I also see it as a measure of setting goals, which can admittedly get out of hand when you focus on “known words” and ignore listening, speaking and writing.