The highlight library used by the highlight plugin has many features that are not accessible through the ikiwiki format directive.  I've created a patch that exposes the line numbering option and opens the door to expose other options more easily.

The [[!taglink patch]] is in a github branch here: <https://github.com/trapperhoney/ikiwiki/tree/linenumbers>

I made a test/demo of the feature here: <http://www.angrydoughnuts.com/temp/ikiwiki/>

And the updated plugin documentation is here: <http://www.angrydoughnuts.com/temp/ikiwiki/html/plugins/highlight.html>