'Která' is the plural form.
If we were asking about a single window, the Czech sentence would start with 'Které...'
And 'which' certainly does not have to be singular.
Perhaps "which one of those windows is yours?" But maybe there is a different way to say that in Czech.
From my perspective (native AmE), since the Czech sentence is clearly in the plural, a plural translation is appropriate. "Which one of those windows is yours?" (suggested alternative) is not the same as "Which of those windows are yours?" (Czech sentence).
Makes sense. How would you say which one of those windows is yours? Would you even want to say it that way in Czech? Btw I'm also a native American English speaker. Cheers