OmniScripts are deployed with version 1 and Templates are not deactivated when deploying.When deploying OmniScripts, you should see in the target org a new version of the OmniScrip created. The new version number should be the corresponding one based on the latest version that exist in that particular org.
If you see that the OmniScrip is created with version 1 all the time, the org you are deploying to might have the "AllTriggers" deactivated under the Custom Setting "Trigger Setup". This custom setting should be active.
Having that custom setting deactivated will also cause that new versions of templates will be created without deactivating the previous version. This can also be reproduced in the org without actually deploying the template.