Here scribe 2 in the printer’s manuscript wrote the name of the city as Jordan, and the 1830 compositor set the name as Jordan. Yet when Oliver Cowdery proofed 𝓟 against 𝓞, he corrected 𝓟 to read Jordon, which implies that the original manuscript actually read Jordon. Both scribe 2 of 𝓟 and the 1830 compositor must have assumed that the biblical spelling was the correct one for the name of this Nephite city.
And Oliver Cowdery’s scribal practice argues that indeed this is the case. We have already discussed a case where Oliver mistakenly spelled the biblical name Jordan as Jordon, namely, in 2 Nephi 19:1, an Isaiah quote. In that passage the text refers to the river Jordan, so the a vowel is correct. And even earlier, Oliver wrote Jordon initially in 𝓟 for 1 Nephi 17:32, but in that case he virtually immediately corrected the spelling to Jordan. (In fact, in 𝓞 for 1 Nephi 17:32 he wrote Jorden for this name; see under 2 Nephi 19:1 for further discussion.) The important point here is that this second case is another reference to the river Jordan. So these two scribal errors in 𝓟 argue that here in Mormon 5:3 Oliver made the same mistake in 𝓞: namely, he wrote Jordon instead of the correct Jordan. Most likely, the name of this Nephite city was the biblical name. For two other examples of biblical names here in Mormon, see under Mormon 4:20 for Boaz (the name of a city) and under Mormon 6:14 for Shem (the name of a Nephite military leader). The critical text will retain the spelling Jordan here in Mormon 5:3.
Surprisingly, in the 1849 LDS edition, the spelling Jordon showed up once more here in Mormon 5:3; this misspelling was retained in the LDS text until the earlier Jordan was restored in the 1920 edition. Orson Pratt, the editor for the 1849 edition, had no access to the manuscripts, so the spelling Jordon in that edition was probably not the result of his editing; it was very likely a typo introduced by the typesetter. Nonetheless, Jordon persisted for some time in subsequent LDS editions.
Summary: The correct spelling for the city mentioned in Mormon 5:3 is probably Jordan, the biblical spelling, not Oliver Cowdery’s misspelling Jordon (which he twice wrote elsewhere as the name for the biblical river Jordan).