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 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