The 1837 edition accidentally replaced the present-tense hath with the past-tense had, perhaps because of the influence of the preceding past-tense transgressed. The words here represent the sinful soul at the day of judgment. These words are therefore in the present-tense except for the reference to transgressions during one’s life. The present-tense hath agrees with the present-tense am found in the following subordinate clause (“that I am a prey to his awful misery”) as well as with the preceding present-tense are (“and my transgressions are mine”). The 1879 LDS edition restored the original hath (perhaps by reference to the 1830 edition); the 1908 RLDS edition most probably used the printer’s manuscript to restore the hath.
Summary: Maintain the original present-tense hath in 2 Nephi 9:46; this passage refers to the words that the guilty soul will say on the day of judgment, so the past-tense had is inappropriate.