For example: "Toto je moje žena Jindřiška a paní Božena je manželkou/manželka (or ženou/žena) mého šéfa." (This is my woman Jindřiška and the lady Božena is wife of my boss.)
WIFE = manželka or we say "moje žena (moje paní, má choť)". For "husband" - "můj muž"
"Která manželka je Žofie?" This sentence is nonsensical.
It is wrong here, because "wife" is translated in Czech as "manželka", and in this sentence it is "žena" that means "woman", not "manželka".
Which wife is Žofie? = Ktera manželka je Žofie?
Which woman is Žofie? = Ktera žena je Žofie?
PS. you have some mistakes: photo album & wives should be correct in English.
Because for "žena " to mean "wife" it has to have a possessive in front of it. Like "moje/my", "vaše/your (formal), "tvoje/your (informal). Without this it means "woman".
The same applies for "muž /man". With a possessive, it means "husband", without one it means "man".
If you want to refer to a wife in general/some random wife without a possessive, you would need to use "manželka", and "manžel" for "husband"
It is not a common practice. Only historically, when it took 3 month to learn about something an English king did would names get changed to local versions. It is true not only about historical people but also about historical places. London is Londýn, Paris is Paříž. But any newer places are keeping their original spelling to avoid confusion. New York is not Nový Jork, but still New York in Czech. Prince Charles and Prince William and Prince Henry are not Princ Karel, Vilém and Jindřich. And neither is Žofie a Sophie. Not to mention there are likely 5 different spellings of this name that we would have to manually edit to every single sentence she is in...