lambeco

Found a solution! It requires access to the following PHP functions:
http://php.net/manual/en/function.parse-url.php
http://www.php.net/manual/en/function.http-build-url.php

…as well as the DOMDocument object.

Once you have that, add a filter for ‘wp_nav_menu_items’ with the following:

function makeDeeplinks($items,$args = null)
{
	$dom = new DOMDocument();
	$dom->loadHTML($items);
	$linkNodes = $dom->getElementsByTagName('a');
	$count = $linkNodes->length;

	for($i = 0;$i < $count;$i++)
	{
		$node = $linkNodes->item($i);
		$url = parse_url($node->getAttribute('href'));
		$url['fragment'] = $url['path'];
		$url['path'] = '';
		$node->setAttribute('href',http_build_url(null,$url));
	}
	return $dom->saveHTML();
}

It basically takes the menu items string, converts it into a DOM object, pulls all the ‘a’ tags and turns the path into an anchor reference.