You can exclude folders or (VSE8.8p7 at least) you can change Scan Items to Specified file types and add the extensions you wish to scan separately in this case JAR, WAR, Zip etc.
It sounds like you will need 2 separate jobs for this.
Job 1 scan everything and untick 'scan inside archives'
Job 2 scan only extensions and leave scan inside archives enabled
I would suggest reviewing the best practices for VSE, specifically page 27. It is not advised to scan archive files during an ODS scan unless absolutely necessary, for the reason you have described which is long scan times. Archives on their own, are benign, and it's when the contents of the archive are extracted could there be a malicious event occur. For that reason, it is recommended to scan archive files with OAS, but not ODS.