Messages in iCloud uses "optimize storage", freeing up storage space used by the Messages app.
Take my iPhone, for instance. On iPhone Storage page of the Settings app, Messages app is currently using 90 MB of "Documents & Data" storage space. On iCloud Storage page, however, Messages is using 1.7 GB of iCloud storage space.
And as
Gyroworld pointed out earlier, iCloud Backup will omit Messages data for backup (ditto for Photos data if you enable iCloud Photo Library).