All the padlocks that I have dealt with, that are rekeyable, usually have only one drain hole as the screw passes down through the shackle hole and then into the base plate which keeps the unit together. An American 1100 series, for example.
If there was a drain hole, there would be nothing to screw into, unless the screw fitted into the back of the core.
Sounds like you are onto something - how does yours fit together? I think that this is exactly how mine fits together.
thanks 🙂