Yes. SealPath can protect several documents all at the same time. Select the documents and drag them to a given protection and they will be protected by it. If for some reason the application was unable to protect one of them (e.g., you do not have permissions to change the protection), it will inform you of this.
You can see how to protect several documents at the same time here.
You can also protect a folder directly dragging it in a protection box or with a "right-click" over a folder. You can see how to protect folders here.