Some means of identifying a paragraph number is essential to avoid confusion. A plain, unqualified number will be assumed to be a page number. The use of square brackets reflects a practical and widely accepted indicator of a paragraph number. This cannot be said of other means of indicating a paragraph number. Square brackets are efficient for typing, use of space and quick recognition.
None is as true of use of the term 'para'.
Square brackets are available on a conventional keyboard, and will survive conversion from one electronic format to another. Depending on the length of the paragraphs, paragraph numbers may be more or less useful than margin letter citations.