The 1907 LDS vest-pocket edition changed the singular hath to the plural have, but this editing has not been followed by subsequent LDS editions. The question is whether “your joy and your faith” should be considered a conjunctive plural, thus requiring a plural verb form in standard English. The use of hath here in the original text does not prove that the conjunct is a singular conjoining of semantically related nouns since hath was used with both singular and plural third person subjects in the original text. The use of the repeated possessive pronoun your suggests that the conjunctive noun phrase is semantically plural.
In the earliest text for the nearby book of Helaman, there are a couple of other conjunctive examples of this same problem involving the semantic number: “there was continual peace and great joy” (Helaman 3:32) and “the famine and the pestilence and destruction which has come unto them” (Helaman 11:15). For discussion, see under each of these passages.
Summary: Maintain the verb form hath in 3 Nephi 1:6 (“your joy and your faith concerning this thing hath been vain”); even if the subject here is plural, the original text permitted the historical third person singular present-tense form hath to take plural subjects.