A full 100% will not be possible but you could switch to iFrame mode instead of the Youtube content mode.
1. Go to Settings > Media and turn on the iFrame option. Save and scroll down to the new iFrame section. Set the width and height to 100% (note that Fancybox will always keep a margin so the result will not be 100% in reality)
2. Modify your Youtube links (use the HTML tab) so they look like this:
<a href="//www.youtube.com/embed/XXXXXXXX" class="fancybox-iframe">link text or image</a>
where the XXX is replaced by the movie ID as it is used in the
?v= URL parameter when you open the corresponding Youtube page.
From now on, the Youtube movies will be played as large as possible in FancyBox :)