They're mostly eyes, which don't fossilize well.

Most of them are still alive. And if they die they don't leave bodies behind. The magical goo they are made out of get absorbed back to their creator.

What do you mean? I was watching a documentary about one just last week.

No body, no crime.

Here you go

Because they're not physical beings and they don't die

There are! It's just that they're buried in the heavens and historically speaking the sky is really hard to dig up.

No bones

'Cause they can all dance on the head of a single pin. So they're really really tiny. Also finding the pin is really hard.

Don't be obtuse.

There are! Angels look like feathered lizards. Unfortunately all angels went extinct 64 million years ago when God made a little oopsie.

Has enough time passes since the uprising to allow them to become fossils?

Also, think about how there were millions of years of Dino's, yet there are so few skeletons.