It appears Speed Optimizer (SO) removes the query strings from the files shown in the JS Combine and JS Deferral exclusion list. Why?
The above sometimes creates issues with other performance plugins which utilize the entire file name (with query strings). If using two performance plugins, for example, jQuery could be cached twice (the file with and without query strings) and create page display issues downstream.
Note: Removing query strings from files is a performance recommendation that was deprecated a long time ago. SO needs to be updated in several areas to reflect this.
Details: Query Strings Deprecated