That will involve some optical alignment considering the actual shapes of the glyphs? I imagine one would get this feeling of not perfectly aligned even when the center of the bounding box of the numbers coincide with the center of the circle.

You could use the box from baseline to ascender instead of descender to ascender. Usually there aren't many strings where that would look imbalanced.

Looking at the actual characters risks having different alignment for different nodes, which would look bad as well.

Most text rendering systems can do this quite well automatically.