Currently projects from a multi-project repository are only available for import by Import / Clone Existing Mercurial Repository, if the eclipse .project file is part of the versioned files.
We currently use Maven in all of our projects and do not check in the Eclipse files which are generated by "mvn eclipse:eclipse" (what seems to be best practice). We use the flat project layout (no nested projects) - we don't use m2eclipse for stability reasons.
We cannot import these projects directly from inside eclipse, because in this case, it creates an Eclipse project and .project file only for the repository root. Afterwards, you would have to delete the project without content, close Eclipse, run "mvn eclipse:eclipse", remove the .project file manually so that Eclipse can then after restart import the projects in the subfolders. For that reason we clone the repository at the command line, run "mvn eclipse:eclipse" and then switch to Eclipse and import all the projects.
What I would like to see is that the Mercurial import is able to create eclipse projects for all folders that contain a pom.xml file and creates simple "general project" configurations based on the folder names. After import we could then call a versioned launch configuration for "mvn eclipse:eclipse" that overrides the .project files with the real ones. Before using Mercurial we worked with Subversive that pretty much did the same thing when selecting multiple folders.
If you detect an existing m2eclipse plugin, it would also make sense to provide an option to automatically enable m2eclipse dependency management for these projects. In that case projects can also be nested.