Although Joseph Smith deleted the it here, he left all other instances of the expletive it in the phrase “to take it upon one(self ) to do something”:
There is only one example of this construction for which the expletive it is not found in the manuscripts:
It is quite possible that the text in Alma 62:44 is in error, that the pronoun it was accidentally dropped as Oliver Cowdery took down Joseph Smith’s dictation. For discussion of this possibility, see Alma 62:44.
There is one other possible example of this construction with it, but here the following clause begins with and rather than to:
In this instance, there seems to be no referent for the pronoun it. The original manuscript is not extant for the and here; thus it is possible that the and (written as &) after you in the printer’s manuscript is in error. A reading with to would provide the appropriate referent for the pronoun it: “and take it upon you to cross yourself in these things”. For discussion of this possible emendation, see Alma 39:9.
Summary: Restore the original it in 2 Nephi 5:9 (“all they which were with me did take it upon them to call themselves the people of Nephi”); all other examples in the text of this construction have been left unedited.