Yes you can still use check-in even if you are not using Whova's registration. If you do not use, it will not prevent anyone from using the app. This feature is available to anyone using the app and is meant to replace paper check-in if that is something that you and your team typically do. The check in is very easy.
You can easily check in your attendees through your dashboard, or through the app if you are an Admin or Check-in Staff.