Short file name support can lead to issues when you're synchronizing/replicating folders and files from multiple machines together into a shared directory structure. For example, you can receive the issue outlined in the article Cannot create a file when that file already exists. The generation and maintenance of short file names also causes a significant negative performance impact on the performance of the file system. If you are not using DOS or Windows 3.1 applications that require the old 8.3 short file names then there is little reason to leave short file name support enabled on your systems.
Modern versions of the Windows operating system disabled short file name generation by default. All operating systems newer than Windows 2008 have this option disabled out of the box. However, that does not mean that short file name generation is off for the volumes on your system. There is a system wide setting that controls if the setting is used on only formatted volumes and a setting for each volume. For example, if you upgrade a volume from Windows 2003 that has short file name generation enabled to Windows 2012 then you will still have short file generation enabled on that upgraded volume. In addition, disabling short file name support does not strip out short file names on files that already have them.
Microsoft provides a means for disabling short file name generation using fsutil. You can also use fsutil to strip the short file names from existing files. Instructions for disabling short file name generation and stripping short file names from existing files using fsutil can be found at http://blogs.technet.com/b/josebda/archive/2012/11/13/windows-server-2012-file-server-tip-disable-8-3-naming-and-strip-those-short-names-too.aspx