Many journals do specify that cover letters are optional. From my experience, most people write cover letters in journal submission, but I am also aware that articles can also be published without the cover letter. Therein arises the question: why are cover letters written if they are not necessary for the publication process? My guess is that perhaps it helps to prevent the desk-reject from the editor.
Prior to online submission forms, cover letters let the authors communicate information to the editors. Information I have included in covers includes:
- Why the manuscript fits into the journal (if i recall correctly, Ecological Indicators explicitly requires a statement of what "indictor" you are addressing in the manuscript)
- Potential reviewers and blocked reviewers
- A statement that the manuscript is not under review elsewhere
- Other pertinent information for the editor such as why the manuscript is timely (for example, perhaps you are studying a species that is under consideration for listing as an endangered species, and the information may be public, but not widely known)
- Responses to reviewer comments
- How I am meeting the journal's open data/open code requirements
With current online journal submissions, all of this information can be captured in online forms. Hence some journals either no longer require cover letters or outright do not allow authors to upload them. Conversely, I have seen other journals that still require cover letters.
I suspect journals use of cover letters depend upon the history of the journal, their current online publishing system, and the culture of the editorial team and office.
I like to see the cover letter as the 'meta' part of your paper. What constitutes as meta is essentially anything beyond the purely scientific aspect of the paper, which can be easily gleaned by reading the abstract (in theory).
This is your chance to speak to the editor personally about your paper. Most basic advice about cover letter writing is emphasizing writing about why (1) your work is important and (2) why it is suitable for this journal in particular.
Even if your handling editor is an expert in your sub-field (and in my experience it rarely is - this is especially the case for general-interest journals), it is not always immediately obvious why your results are important, or even interesting. All scientists know about the 'hot topics' in their field, usually because they are published in high impact journals. But how did these topics get published in the first place without getting the recognition first? Usually some degree of convincing is needed.
There can also be other reasons for including a cover letter. Perhaps you may have spoken to the editor at a conference and you want to remind him that this is the paper you were talking about for submission. Or perhaps your paper was transferred from another journal and you want to inform him about the comments from the reviewers there. The cover letter can also be the place where you recommend reviewers for your paper.
It is easy to think for the writer that the merits of one's paper is obvious, or why waste your time? But this is not immediately obvious for the editor, who generally has a limited time to make a decision.
I am also aware that articles can also be published without the cover letter.
The cover letter is not intended for the reader.
Therein arises the question: why are cover letters written if they are not necessary for the publication process?
There is far more to the publication process than what sees print.
The point of a cover letter is to introduce your paper to the editor of the journal and (potentially) the reviewers. It helps to frame the paper - why you think it's interesting, why you think it's interesting to that journal, and if there's any relevant information that might weigh on the decision to publish, or how to go about publishing it - for example, in biomedicine one might occasionally make a request for expedited publication for information relevant to an ongoing outbreak, or attempt to coordinate a publication's release date with the presentation of the paper at a major conference.
Some journals also use cover letters as a place to put in some boilerplate assurances, like the paper not being under consideration elsewhere.
There is no point in these letters per se.
I presume they are there because of historical reasons, where people were actually submitting the manuscript with a physical letter, so obviously, you would need, back then, to have a cover letter to explain what is the intention of the parcel. But now we can communicate the same information with an email or an electronic form, serving by itself as a cover letter, i.e., giving possible important information to the editor in charge.
Depending on the journal and/or field of research the title and abstract may not indicate clearly the topic or area of interest addressed by the submitted paper. Also consider that the editor may not be expert in the area that the paper addresses.
Are you submitting a paper to a journal that publishes a range of topics?
Are you submitting to a journal that publishes exclusively in one field?
Are you submitting to a journal that publishes exclusively in one area of one field?
Highly sought-after journals such as Nature and Science publish across a wide range of fields, so you would need to provide some specifics as to why you seek to be published in that journal. Also, why they should consider your submission (is it ground-breaking?).
You could submit to a journal that publishes exclusively for one field (physics, biology, chemistry, education...) but with so many areas of research in these fields you could not expect the editor to just know whether your paper is relevant, or which reviewers to assign.
So a cover letter can help define this for the editor - why you have selected that journal, the importance/relevance/originality/defining outcome of your paper, why they should publish/consider publishing your paper. It gives you a chance to give an outline with detail that may not be relevant in the abstract but goes towards background information so that they don't need to read some/all of the entire paper to make a decision.
Actually, if they need to read the whole paper first they may reject it without review, since at the least they may need to read title, abstract and introduction. A cover letter can save them time, which will be appreciated and help your chances of getting the paper reviewed.