If you do this then in version.php, declare that they depend on each other (https://docs.moodle.org/dev/version.php). Some examples: filter_embedquestion and atto_embedquestion, qtype_opaque and qbehaviour_opaque (code of all these is in the plugins DB.)
You are right to think about the database strucutre (and the code structure). It might be a good idea to decide that one plugin is the main one, which is responsible for storing the data and containing the main back-end code which both plugins share. Or there may be some other natural way to split things up.