That would be the quickest and easiest option.
Not sure if I would encrypt each folder before storing it on the NAS though.
Probably I would just create an encrypted file container directly on the NAS that is large enough to fill the drive, then mount it as a virtual drive on the client computer.
Then anything you copy onto the virtual drive would be automatically encrypted and stored to the NAS.
It also saves you the trouble of remembering multiple passwords for multiple folders; you would only need remember one for the entire container.