Do parentheses inhibit clarity? They do and they don't, it's all down to individual use. When used well and skillfully, parentheses fulfill a function that no other punctuation or construction can quite imitate. Their function is similar to em dashes (a woefully overused punctuation mark) and can also be used to mask off digressions (which can detract from the text).
Overuse and use to mask bad habits have given parentheses a bad rep. Long parenthetical statements that don't flow well are a misuse. If the sentence or paragraph doesn't flow when reading it (because of the parenthetical statements) then you're not using them right. Maybe parentheses are the wrong tool in a case like this.
However, just because parentheses are misused often doesn't mean there aren't good ways to employ them. I wrote a longer blog post about this very subject, but here's the money quote in the article that illustrates the central point:
[General Washington] had not done well farming despite all sorts of theories about river mud being the best of manures (it is not), and the invention of a plough (shades of Jefferson!) which proved to be so heavy that two horses could not budge it even in moist earth.
(Gore Vidal, Burr, 1973)
See how well that flows? Dashes would introduce awkward pauses into the writing, rephrasing it entirely would remove the narrator's great sense of self-importance. This novel's narrator is opinionated and talky, but the author cleverly turns his asides into parenthetical ejaculations of color that don't interfere with the flow of the language.
Parentheses can be a useful tool in situations where writing the sentence without them would make the sentence longer, a maze of twisty corridors, or perhaps just drain it of life. Those who learn to use parentheses well have access to a wonderful tool.