As explained under 1 Nephi 22:4, Oliver Cowdery frequently mixed up whether and whither in the manuscripts. Here in the printer’s manuscript, he originally wrote whether but later changed the e to i (the overwriting is with heavier ink flow). Obviously, Nephi departed out of the land, so there is no question about “whether he went”. Instead, the question is where he went.
Summary: Maintain whither in 3 Nephi 1:3 since the text is questioning where Nephi went, not if he went.