In Marketo, is it possible to change the way assets are referenced in Program, Smart Campaigns, Smart Lists, Emails and Reports, or how they are labelled or shown through reporting?
No, it is not possible. The naming convention of assets and how it is used in Marketo is apart of the design of the product.
When assets are created within a Program the naming convention is in the format of ProgramName.AssetName
This is to identify where the asset resides in which program.
Otherwise, multiple assets created with the same name would be causing confusion to the system when referenced in any of our Smart Campaigns, Smart Lists and Reports.