There have indeed been cases of dataloss where AV software has corrupted Cab files or dvs files and the customer did not have backups to restore from or the files were corrupted in the backups. Oplocks is an issue with any SAN storage used for indexes.
The directories mentioned for excluding, would this include on the file server too if file archiving is being done. For example, would you exclude the program file directory of EV on the file server. Or would the ExcludedExe reg key take care of this if you had the executable from your virus software included?
you wouldn't need to exclude those directories (as you're probably going to have a mix of shortcuts and real files, and thus need to protect them), however be sure that whatever AV scanner you use can deal correctly with offline files. In addition, add the AV scanner's exe to the excluded key to CYA.