if an acoustic guitar nut were misaligned-would that cause her tuning to be out of wack?? or hard to stay in tune???
In what way would it be "out of whack"? If the nut slots are cut improperly, it can cause binding and such, this can affect tuning because when you turn the tuning knob the string gets "caught" in the slot and may read falsely, and then it may "let go" with a little pinging sound and then you find it's out of tune....
If the nut is angled badly on the fretboard side, it could cause intonation problems...That would be pretty rare unless some do-it-yourself artists had tampered with it.

Finally, if the nut were actually loose in it's slot, it could move around during tuning... Again affecting intonation.
But nuts are pretty simple.....