Personally I’d say it was simply a matter of a negligent priest who failed to enter the relevant records at the time. I have seen it elsewhere. Sometimes the priest remembers some of the details eg father’s name but not the child’s and relevant gaps are left. Probably intended to fill them in later but never did.
I can’t see any obvious link to the famine (which in any case really only got bad in 1846). Children were still being born all through the 1840s, so that’s not going to explain them being missing from the baptism records.