When a wife asks her husband, "is YOUR daughter home yet?", does this make you conclude that she isn't THEIR daughter but only his?

Not necessarily.

The stressing of "your" in this sentence is more likely a expression of slight annoyance at the tardiness of the daughter than the wife implying that she is not her parent. "My kids when they are good, your kids when they're naughty" is a rather common occurrence

It can also be (depending on context) that the daughter went to the husband for permission to go out that was previously denied by the wife - husband granted permission with a time limit and now that she is late, the wife is placing accountability on the husband for that - but not overly worried.

Example: D = Daughter, W = Wife (mom), H = Husband (dad)

D: Hey mom, can I go out with my friends for dinner and a movie today?

W: No, you have to be at school early tomorrow for [insert appointment here]

D: Dad, I want to go out for dinner and a movie with my friends, but mom said no... please, it is the premiere...

H: I don't see any harm in letting you go, just be back by 11, ok?

Then 11 comes and goes, daughter is nowhere to be seen. After a while, W asks "Is YOUR daughter home yet?"