How likely would it be that a practitioner of ninjutsu in ancient times, when caught, would attempt to maim, (or with a lucky shot) kill their potential opponent with a throwing weapon? Or is it more likely they would switch to another concealed weapon that may do more damage?
Secondly, if they were to so do so, which would be a more common usage, the shuriken or the kunai?
/ducks for the incoming flamage!
Okay, let's look at this from a few angles.
First off, weapons such as Shuriken are not exclusive to practitioners of ninjutsu, they were also very much samurai weapons (and, let's not forget that "ninja" were often samurai themselves, just working in a certain fashion at that time). Next, these weapons were not really designed to maim, or kill, and were not suited to such usage at all. They were primarily distractions in order to either provide an opening to go in for a finishing action (such as in Negishi Ryu, a samurai Shuriken system, or in the classic story of Musashi against a Kusarigama wielding opponent... he threw a short sword or other small blade into their chest when he couldn't get past the chain, then moved in and employed his sword to kill the other warrior). So how likely? Not likely at all, really.
The Kunai itself is not a Shuriken, nor typically thrown. There were forms of Shuriken which were known as Kunaigata, used in a few systems, but they were not really Kunai, just named for the shape of them.
Finally, you need to understand what the primary reason for the use or employment of such weapons would be. Within the Bujinkan/Genbukan/Jinenkan traditions, the best known use of Shuriken is from the Togakure Ryu, although it also features in Koto Ryu, Kukishinden Ryu, and a little in some others, such as the origin story of Takagi Yoshin Ryu. Within Togakure are the only formal kata for the weapon, though, with it being either Kuden or Henka in the other ones. Within Togakure Ryu, the employment of Shuriken (Senban in this case) is pretty much exclusively for escape, so Shuriken should be looked at (from a ninjutsu perspective) as a distraction primarily, not a "damaging" attack.
Hope that helps clear some things up.