Merging apache-2.0.43-r1 didn't install any modules (mod_*.so). They should have been in /usr/lib/apache2 (as they were in apache-2.0.43) but they weren't installed at all. ...And there is no earlier version of apache2 in the Portage tree, so I can't step back a version to fix my b0rked webserver :-(
Aha, problem solved. It was the fact that /usr/lib/apache2 was a symlink to /usr/local/apache2 (from an old manual installation) and although Portage claimed it was installing files, it refused to install anything into /usr/lib/apache2 (subdirectories were fine, strangely). This looks like a portage bug, and as such I've filed bug 14331.