Is there any RMarkdown "ioslides-CSS" reference guide?

To answer your first question:

<style>
slides > slide:not(.nobackground):after {
  color: green;
}
</style>

About the second one or how did I come up with the answer to the first question:

There is no reference per se. The problem here is that the appearance of the slide numbers is defined as a pseudo class (such as :after):

If you click on that line you find the corresponding styles for that pseudo element:

You can clearly recognize the definition of the slide numbers within the attribute content. So this CSS affects not the slide element but the space "right underneath" it. Just copy and paste the CSS selector and add or edit the styles you need.

In such situations, if I cannot see the forest through the trees, I usually check the default stylesheet which can be found at github. If you Ctrl + F for :after (knowing that it possibly is defined as such) or just slide-num you will find the corresponding lines of code pretty fast.