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For example,

The model shows a great divergence at zero momentum (see Fig. 5(c))

I am not sure if the last two "))" appear cluttered. I have seen suggestions of using [] on the outside but I have never seen any examples like that in academic writings. What should I do?

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    This paper has an example of using "[Fig. 5(c)]". However, that's not necessarily an endorsement. Basically every variation you can think of is used. Sometimes multiple in the same paper. You can view some examples via google search. In my opinion "(see Fig. 5(c))" is fine, however, you should check if any style-guides apply to your paper and whether they have something to say on it.
    – user54131
    Commented Jul 19, 2022 at 16:10
  • Have you considered using "5c" instead of "5(c)"? Or is the numbering scheme specified?
    – Stuart F
    Commented Jul 21, 2022 at 13:57

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Your example is fine.

If the rest the document uses normal parenthesis for references, changing to square brackets for one reference because the reference has parenthesis will just cause confusion.

If you are doing this, though, you need to rewrite your sentence:

This is a sentence (with a parenthetical addition (which itself contains a parenthetical addition.))

That means you are trying to stuff too much information into one sentence. At that point you need to ask yourself if the additional information is needed. If not, leave it out. If it is needed, write it in properly. It may take an extra sentence, but it is clearer.

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This is largely context dependent and opinion based, however there is one rule: Readability. As per the answer to This English Language stackexchange question about spaces, so what is the most readable style in your usecase?

Though a programming language guide, the MISRA C guidelines may provide a small amount of help due to excessive use of them in that language. As a rule it suggests excess use of spacing so that you can more easily pair which set are linked, however I personally think this looks robotic (though I only use it on computers (which makes a difference I geuss?) ). Take the following example:

The dog (which was quick (and brown))

This example isn't that relevant for much, as is the paragraph about MISRA. However between the two uses of nested parentheses in this, which feels more natural? For me it's the one about the dog, though if you need it very clear where the parentheses cover, I would add the space or mix square brackets and parantheses [like so (1)].

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In text, you could try using commas or dashes for one of the sets of parentheses. Commas may not give enough sense of subordination. Dashes add emphasis, which may or may not be useful.

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