FL-1825: change vala dep to 'vapigen(+)'

Change the vala USE dependency string to assume that vapigen is enabled
if not in IUSE. It is built unconditionally starting with vala:0.26.
gnome-boxes: fix kernel checks

Perform kernel checks only when kernel sources are available, and add
a missing call to determine the kernel version. Fixes Gentoo
bug #504822.