I think that the stripes selection means "apply no custom color to this nick but keep the normal nicklist/text/nick color" and not "make this nick transparent".
Actually, in mirc, color 99, or "transparent," just means that it uses the normal text color. For the nick colors, mirc just looks at the $color(normal text) and uses that for such nicks. You can test this by changing the color for normal text in the colors dialog, alt+k. $cnick(N).color will return whatever you set it to.
Now, this doesn't seem to me to be a bug as such; it seems to be the way that khaled wanted it. However, I do think it ought to return 99, so that you can do scripting of such things as join/part events and color them in an appropriate way without too much trouble (ie, one line of code that does any color, including none -- this way, the color 99 one is a catch-all that only triggers if no other rules do.) That sounds like a feature suggestion to me.
