I think your, convoluted, example would be better if you hadn't merely added in parentheses randomly. Parenthetical and asides are sub-statements, and, typically, can be omitted without losing the overall meaning of the expression.
Take my above asides ", convoluted," and ", typically,". Neither are necessary for understanding the sentence, but neither make the sentence exceptionally difficult to understand for a literate reader.
The method in which parentheses (and other structuring notations) are used is more akin to grouping from algebra and mathematics.
EDIT:
Original:
OTOH, following something (say, an English text) (which is heavily parenthesised) may be (I'm sure there is a lot of references to back this notion) exceptionally hard (even if there is just one nested level (and more levels certainly add more confusion)). Choosing flat over structured often makes a lot sense.
But it doesn't make sense when we remove the parenthetical statements:
OTOH, following something may be exceptionally hard.
Choosing flat over structured often makes a lot [of]
sense.
(one edit for clarity). That first sentence has lost all meaning. Following
what? Following a car on foot can, indeed, be exceptionally hard. But following a slug is often exceptionally easy.
A more reasonable version of your sentence:
OTOH, following something--say, an English text--which
is heavily parenthesised may be, I'm sure there is a
lot of references to back this notion, exceptionally
hard (even if there is just one nested level (and more
levels certainly add more confusion)). Choosing flat
over structured often makes a lot sense.
Now the remaining asides (demarcated using the various English notations of em-dash, comma or parenthesis) can be removed without losing the general sense of your sentence.