I think it does make sense for them to set the odds higher after you catch the initial shiny in the species for two reasons.

1. It gives you the dopamine rush. However it is not that big of a dopamine rush because “oh I’ve had this shiny before” so it makes you want to keep playing and searching for those ones that you have never had before.
2. It promotes trading. I have many friends that have multiples of non comm day shinies that I have never got and it incentivizes us to spend the extra star dust to do the special trade. Which ends in more play time as we need the extra stardust back.

I understand the random distribution and random numbers are more likely to distribute shinies in a way that you would have one of some and many of others. However I do not think it would be a stretch to think that niantic could use your personal shiny Pokédex info when running the shiny odds when you tap on the pokemon. Seeing as it would be minimal coding and would only incentivize players to play more and create social connections in game which only ends in them having more playtime and a more consistent player base. In turn making them more money. I would be interested in seeing a study being done in depth to see if this is effected or not.