Mandatory reading: How does KiCad know which symbol pin represents which pad of the footprint?
Connector footprint pads are numbered as defined in the datasheet of the connector. Meaning if the connector datasheet uses 1-2-3 then the footprint will use the same numbering scheme.
The reason there are different numbering schemes present in the symbol lib is because different connector manufacturers use different numbering schemes for their connectors.
The way to choose a particular symbol for a component is by looking in the datasheet which numbering scheme is used. This ensures that the datasheet, symbol, footprint and markings on the connector agree with each other.
In the case of pin header there is not really a definition given in the datasheet. As far as i am aware there is however a kind of standard way these are normally numbered. They use one row for all the even pins and one for the odd pins.
This might be the case because flat cables are often connected to such parts. Such flat cable connectors are physically build such that odd numbered leads end up on one row and even numbered ones on the other. (Yes i know shrouded headers are normally used for such cable connections. But they are similar enough to each other such that it makes sense to use the same pin naming scheme for both.)