I admit I have a hard time accepting that a crossed out baptism is a "birth that did not happen"... I don't imagine people arranged baptisms before a child was born since they couldn't know when the child would arrive (even with modern tools due dates are a best guess). I might accept that the child was born, the parents gave the details to the priest in preparation for the baptism, the child died before the baptism was performed, and the priest erroneously entered the baptism in the register from his notes, realized the error and struck it out - a baby still would have been born.
In an unsuccessful search for an authoritative answer on why a baptism would be struck out:
A) I did see a mention of a priest who recorded baptisms in a 'day book' and later transcribed them into the baptismal register (don't know if this was a standard practice, or just something this official did) - he struck out a number of register entries when he realized the baptisms he copied were from a day book entry in a previous year.
B) I also noticed that the LDS completely removes excommunicated persons from their records, leading me to wonder if other denominations may have struck out entries in baptismal registers to denote a person had been excommunicated?
C) Another thought I had was that it might be a way to differentiate a 'lay-baptism' from one performed by church officials - while they were (and are) strongly discouraged, they were permitted in emergencies and had to be reported and recorded.
D) I also had a glance over some current Sacramental Records handbooks (mostly RC) for ideas on when a baptismal record might be crossed out - I noticed a statement that the parish that performs the rites keeps the official record, but if the person has a different home parish, the home parish may keep by an unofficial duplicate record - perhaps crossing out a record is a way to indicate it is the duplicate and that the event occurred elsewhere - I have seen something similar used in some civil records.
Again, the above is just my thoughts/speculation - Hopefully someonefamiliar with the conventions of Colonial baptismal registers will see this comment and add to it.