Quoting Wikipedia, "In any given year, the impact factor of a journal is the number of citations received in that year by articles published in that journal during the two preceding years, divided by the total number of articles published in that journal during the two preceding years".
Accordingly, self-citations (by an author, by a journal, or by both simultaneously) are not excluded in the main metric. It is true that in some cases self-citations are discarded (for instance when comparing journals or manuscripts), but it would be ludicrous to exclude, for instance, the New England Journal of Medicine self-citations, and this applies to all reasonably good journals, whose ranking remains stable excluding them:
Regarding your questions:
Impact Since B is related to A, I will probably submit it to the same
journal. Would this help the journal's metrics?
Yes, it is common practice among researchers and journals.
Lets say paper A currently has no citations. Would they be reluctant to
accept paper B (quoting A)?
No, as long as the citation is appropriate.
Also consider that a citation increases the likelihood of your article A being looked afterwards by other researchers and quoted subsequently, and that an overlooked article can always become a sleeper hit.