Mhh, do I keep/manage older versions, aehm no! o) I sometimes keep a seperate version as long as I improve a specific one. While doing so, I tend to rename the "stable" version to *.dis, to prevent DO from running it. If the script to be enhanced is done, I delete the *.dis version. For anyone updating a script by SW, an archived version (with version number appended) will be stored in "/script addins/archive" - in case you didn't know, so nothing get's lost. To check what versions are active and running, I use the "ScriptDetails" columns, they work in any directory and maybe they are of use for you too: Columns: ScriptDetails (update status of add-ins etc)
So, I think you can still call your old scripts the way you like, it's just the uploaded/updated version that needs to apply to the same name. Just like it is for "DOpusInstall.exe", new version - same name. It think it also helps to prevent duplicates in "/script addins", if people download scripts from here and put them to work.