There are no downsides using namespaces, we have built them to solve the organizing problem. We use many workspaces on a daily basis.
You can move repositories as often as you want, but keep in mind that the namespace is part of the repository url and you have to adjust all places where the url is used (e.g.: clones, build jobs, ide configuration etc.).
To move a repository to another namespace, ensure you have selected the "custom" namespace strategy in the administration. Then you can hit the rename button in the repository settings, which should now have a field for the namespace.