Caveat emptor: not a native speaker. But I believe you are correct, that would be the strict translation of the present perfect.
However it is apparently customary in spoken German to use the present perfect in place of what English speakers call the simple past tense, cf. the last paragraph of http://german.about.com/library/verbs/blverb_past.htm
So this sentence means the same thing as the more technically accurate "Saht ihr sie?"
No, that is not correct.
The definite article "the" in "the correct translation" implies that there is exactly one translation, and that is not true.
"Have you seen her?" and "Did you see her?" are both correct translations of Hast du sie gesehen?.
"Have you seen them?" and "Did you see them?" are further correct translations.
The usage of the German Perfekt tense is not the same as that of the English present perfect tense, but is wider. Saying that German Perfekt corresponds only to English present perfect is incorrect.
Yes -- in a question like this, the verb is (almost?) always followed by the subject.
A bit as in English, where we might say "Does she know him?" but never(?) "Does him she know?".
So the subject ihr comes first, then the object sie.
(And pay attention to the capitalisation -- this sentence uses sie, not Sie!)