I wouldn’t recommend creating a ton of Structure sections, because the administration workflows and UI are just not suited for having lots of identical sections.
Here’s a basic model of how you could organize this in Craft:
- Create two Sections called Issues and Articles
- Create an Entries field called Issue Articles, with the Articles section selected.
- Edit your Issues section’s Entry Type, and add the Issue Articles field to its Field Layout.
Now, each issue will be represented by an entry within your Issues section, and each article will be represented by an entry within your Articles section.
Thanks to the new Inline Element Creation feature in Craft 2.5, you will easily be able to define new articles right from the Edit Entry page when creating/editing a new issue, via your Issue Articles field.