The 1907 LDS vest-pocket edition changed hath to have, perhaps because of some grammatical notion that the subject “any of them” is plural. However, Merriam Webster’s Dictionary of English Usage provides considerable evidence that in standard English any can be treated as either singular or plural (see the discussion there under any). And of course, the original text itself generally permits considerable variation with respect to subject-verb agreement (see, for instance, the extensive discussion under 1 Nephi 4:4). As far as the original Book of Mormon text is concerned, there are examples of both singular and plural any (although most examples take singular verb forms in the original text):
Since variation is possible, the critical text will in each case follow the earliest textual sources in determining whether a singular or plural verb form should occur with the subject any.
Summary: Retain the original use of the historically singular hath in 2 Nephi 25:9 (“and never hath any of them been destroyed”).