On Apple Podcasts, the best practice is to NOT include the season and episode number in podcast episode titles because this is taken care of by the season and episode tags. However, a lot of other podcast apps don't automatically add the season and episode number to the title.
In order to cater for the best practices for all apps, it's possible to send two different titles with your Omny RSS feed.
In the RSS feed there is an <itunes title> tag (without the season and episode number) and <title> which can include this info.
Here's an example of how the format would look:
<itunes: title> "my episode"
<title> "S1 E1 my episode"
To activate this feature and to customise and set the best format for your RSS feeds, you can head to program settings - content - RSS format.
Choose your preferred style from the dropdown menu, click save changes and you're done!