Is there any way to enforce a naming convention for files uploaded to SuperContainer? I have another process reading the stored files (not through SC) and I'd like to make sure the uploaded files don't have certain characters in their names: !@#$%& and so on.

I'd advise against accessing files stored in supercontainer for a number of reasons. You should think about data stored in SuperContainer as data stored in a filemaker container field, and I recommend only accessing it through a filemaker or script-controlled interface the same way you would as if it were stored in the database directly.

If you do so, one of the benefits is that you can control naming and access to files like you are trying to do. The SuperContainer Companion plugin allows you to rename a file on either upload or download using SCSetContiner and SCGetContainer, which would solve this issue for you.