Basically what title says - are any of you aware and could point me to a story, where after her ascension Twilight has batpony wings?

I am not, but such a story would certainly merit a look.

I think there was one where she got draconic wings... But it was many years ago, and it's unfortunately buried somewhere in one of my lists. Either that, or it was put on permanent hiatus,

Can't think of anything where she gets batpony wings from her ascension.

Maybe not quite what you're looking but there is Sun Stiletto
She turns herself into a type of vampire that is immune to sunlight and gets bat wings in the process.

6713869 No, but here are a few images for you:

https://www.fimfiction.net/story/131034/second-princess-of-the-night