Develop a system of folder organization from the very beginning of your use of Acoustic Campaign. Too much data is not the problem. The problem is how much data is on a single page.
You have your own business rules that make the most sense to you on how to structure your folders. Perhaps by year, or by the type of communications, or if you are an agency, by client, etc. Within folders, consider subfolder structures. Try to keep individual items per page under 50 (or no more than 100). Once you have items within each folder down to a manageable amount, you shouldn't get that script warning anymore.
You don't have the ability to create folders in the reporting area directly. Reporting is organized under the Sent tab under Content > View emails > Sent. Once the Sent tab is organized, it will be reflected in the reporting area under the single email reports and comparison reports.