Application Naming Convention

We have an old application that we are in the progress of replacing with a new one.  This is being done by a consultant.
This old system used a fairly basic naming convention but one I believe is fairly standard (perhaps with SAP).  Anything that was customised by us was prefixed with ‘Z_’.  This might be a report, query or a security role.  This was the only naming convention that was strictly adhered to and one we inherited from previous employees and just carried on using.  One benefit of this was that when it came to update time (which stopped a long time ago), we could easily see what was customised and therefore made sure they weren’t removed as part of any update.  There was also a naming convention that wasn’t really stuck to for user roles where further information would be added after the Z_ to perhaps indicate a department or team.

The consultant is in the process of creating reports, security roles etc in the new application but has no plans to use a naming convention, which was a surprise.  Are there any serious usability or security issues associated with not using a convention?  Ideally I would like it to be agreed and implemented asap before too much customisation has taken place but want to make sure it is a point I really need to be ensuring is implemented or one I can forget about.