Sometimes a mnemonic is written in parentheses and sometimes not. Is there any significance to when the parentheses appear or do not appear?
There does not seem to be any significance to the fact that some Simanim appear in parentheses and others do not. The Simanim are found even in the early manuscripts of the Gemara. In the very first editions they were separated from the text with other punctuation marks, seemingly to show that they are not part of the Gemara's text. In some places, Rashi is also Mefaresh the Simanim.