Messages is for all
incoming messages unless you separate SMS and MMS under Options. That includes all email (BES & BIS), SMS, MMS, PIN as well as saved browser requests, saved web pages, call logs if you enabled call logging, etc.
Again, it depends on how you use your BB and how you want it set up. If you're on BES and not using Empower's app to create a separate icon for BES mail it's probably a bad idea to hide Messages. If you rely on saved browser pages/requests or use the call logging feature in Messages it's probably a bad idea to hide Messages.