Hmm... Interesting questions, will see what the experts have to say about this.
My take on this would be to say "yes" because what we call spacetime atoms are more or less Planck-size chuncks so they have a fixed volume, and the larger the total volume, the more "atoms" there should be.
One qualification though : as you said, we are talking about
spacetime atoms, and spacetime doesn't expand or change in any way, it is just "there".
But my understanding is that since patial volume is quantized in QG as well, it may be meaningful to talk of "an increasing number(*) of
space atoms", or of spacetime atoms intersecting a given (expanding) spatial volume.
And lastly, I think the talk of atoms here, while suggestive, does not refer to something as concrete as ordinary atoms, rather as you say it is a way to talk about the "discreteness" of spacetime.
(*) provided we can meaningfully talk of "number" here: what does it mean to count atoms of space, other than measuring a volume?
Edit: this piece by Smolin, published in Scientific American, may be of interest to you here :
Atoms of Space and Time