I'm really confused. apologies if this is explained somewhere, however I have 2 stables , one is full and the other hasn't been used at all. but some of my pets in my nursery still vanish, as the game states they will with no room, despite having that second stable.

Which pets are you referring to? I checked AS & your latest released pet were from 2020.
& I'm assuming this is recent.
It's also possible you have your hatchery settings "Auto Release Un-Named Pets" on.

howdy! i went through your youngest pets and found this zolnixi and this nytekrie who were both from within the last month.

is it possible your pets automatically entered your stables and you just lost track of them?
its a little difficult to tell what is missing other than going through IDs, do you remember what disappeared?

I had a few scale shop eggs before those that just? disappeared. I looked through each tab and nothing, and not in my secondary stable either,

would any of them happen to be these three? i know scale shop eggs are labelled as "tamed pets" which is a little weird.
faelora, aurleon, lupora

if not i'd definitely ask krin about it, he might be able to see your purchase from the egg shop and hopefully find out what happened to them.