Like if I got a shiny milcery with the strawberry sweet and spun it around in the vanilla and ruby swirls, would the pokedex / Pokemon home count them as shiny alcremie with the ruby and vanilla swirls or just its shiny
There are 7. While each of the 64 can be shiny, the shinies are exactly the same in terms of colour -- the only variations are in the Sweets, of which there are 7.
Depositing any Alcremie will show you all of the deposited flavor's sweet variants even if you haven't deposited that flavor + sweet combination into Home. The same applies to its shiny.
I had deposited a shiny Salted Cream + Love Sweet Alcremie into Home. When I check Home's Dex, I can see all of the shiny Salted Cream forms even though I only deposited that one.
If you want every flavor to be shiny, you'd have to deposit a total of 9 shiny Alcremie, each with a different flavor.