It looks to me like this illustration is attempting to replicate the 3-D molecule models that students use in the classroom, hence the circles around the atoms and the smaller hydrogen atom. In your braille graphic, you can ignore the circles around the letters, and the sizing is of no importance.
The shading is something I have never seen before. I think it is fine for you just to mention in a transcriber's note the fact that the rings are shaded in print.
The 2-dimensional orientation can be "tipped" which will allow you to use some horizontal and/or vertical bonds, along with a few oblique bonds necessary to complete each ring. The partially hidden hydrogens are, again, the print copy's attempt at making this appear three-dimensional. This is the CH3 molecule, so just make a carbon with three hydrogens, each with a single bond.
These bonds aren't really accurate. Just braille what you see (make them all single bonds). I think this is just a general illustration, not an accurate chemistry book as you say.
... Regarding the other page not shown, I'm not familiar with what you describe ("some of the circled letters are shaded around the letter itself within the circle"). I need to see the page in order to make a judgment -- can you attach it, too?