Since this is an application that's independent from Kodi, you can install or uninstall it as you please, but there have been reports that after uninstalling Folder Mount, the Android device would go into a bootloop especially when the Folder Mount was used with system folders and unlinking without taking the necessary steps to correct this will get you into a bootloop.
Yes, you can uninstall the application, but make sure that there are no system folders linked to SD.