PKHeX emulates the retail games and continuity.
Gen 1 does not have shinies, but Gen2 does. Since gen 1 was only released on the virtual console, we are considering gen 2 shininess to be ret-conned.
We believe that when the official transfer method becomes available, no pokemon migrated will be shiny.
Refer to issue 247 on github, which also includes discussion in regards to showing gender for RBY files.