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Honestly, I don't think the value of shiny pokemon will decrease at all.
>But getting shinies is a lot easier now, might as well breed me shiny Phiones kek
The reason I don't think it'll decrease is simply because the owner of whatever shiny pokemon he/she hatched via MM is going to be worth a LOOOT more to him/her than an instacheck hatched shiny. Like some anon said, not having your OT on your own shiny is a let-down, and no matter what anyone says, a randomly hatched shiny is something no one will ever undervalue at all.
>TL;DR: Shiny values are relative. Random ones are praised, Instacheck ones are meh