I couldn't find an option for the messages, but I did find it weird that the messages did appear under skulltag and odamex. So, when in ZDaemon, I was playing around with tehe tilde key. Somehow this brought the messages back.
this doesnt relate to ide - it is zdaemon configuration. try to look for it in zdaemon menu (messages). there is also simple method - delete zdoom.ini file in zdaemon folder and reset all your game setting to default