Hi Jan,
You can map and migrate lookups. For more information, please refer to the following:
Mapping Columns
www.metalogix.com/.../mapping-columns-(public-folders).html
Also, please refer to the KB article below to know what is column mapping and when you can use it.
metalogix.force.com/.../Using-Column-Mapping-in-Content-Matrix\\
In addition to this, if you want to map lookup columns and transform them into managed metadata, you can do so. For instructions, please refer to the KB article below.
metalogix.force.com/.../How-to-map-columns-and-transform-them-to-Managed-Metadata
Regards,
Bianca