You can’t change the size of the pencil on the vector layer because each tool has a distinct usage and is therefore limited to a certain way of working.
The stroke of the pencil tool is, when exported, invisible. It’s original purpose was primarily for shading and filling characters in your animation and because of that, the size of the stroke has no meaning, I say “original” because we haven’t worked on it much since then and consider the vector layer not a priority to work on right now but the idea still holds true.
My thoughts are that the pencil tool in Pencil2D vector tools is aimed at making sketches. That are then inked in using the pen or paintbrush tools.
You can of course select it using the selection tool and then fill it the area within the pencil line.
You can use the smudge tool to edit the path of the pencil line of course.
You can hide the line by selecting it any applying a colour with an Alpha Value of zero.