Backup Exec would not be the one locking out connections, that would be Exchange. BE makes a call to Exchange and gets the response from Exchange, BE cannot control what Exchange does. In response to your questions, I would assume that your app is querying Exchange while Exchange is responding to BE to process the backup.
I run anti virus realtime all the time and have no issue with Exchange backups. However, some people have had issues and use pre/post commands to shut down the anti virus software while the backup runs and then automatically restart it once the jobs completes. If you are having no problems with your backups, don't worry about shutting AV down.