My research is on specific publications and their publishers. Should I include all articles mentioned in the bibliography?
Generally speaking
If you are referring to particular content of particular issues, you should cite them.
If you have a database of the contents of the magazines and you work with that, then ideally you publish the database, or in any case explain how you created the database and what was included. In that case you would cite the database, if published, or otherwise refer to it, but you would not cite specific articles unless you use their particular contents, as per the first paragraph.
What are the notes?
In your question you mention that individual articles have been referenced in the notes. Are these notes a part of the dissertation or something distinct?
If you dissertation is a collection of articles and these notes are the articles, for example, then you are presumably writing an introduction that ties them together. Then the introduction would cite whatever it mentions, but likely not very many individual magazine articles, as the details would be left to the research publications.
If you mean some kind of notes you have written for yourself and not to be published in any way, then they don't matter for the question of what to cite in the dissertation itself. The dissertation should stand by itself, without needing private information.