If I remove a namespace from the configuration file, will all the data in that namespace get deleted?
No, if you decide to reuse the storage device for a different namespace, you will need to either delete the file or follow one of the methods discussed here: Zeroize Multiple SSD's Simultaneously.
If the data was persisted, then it would be preserved unless if it is overwritten or the storage is reused, of course.
Also, note that, at this point, in order to add or remove a namespace from the configuration file, you have to shut down all the nodes in the cluster, make the change, and then restart it.