The decrease in bioball use is directly proportional to the efficiency of protein skimmers... as they became more and more efficient at removing waste before it could break down, the need for the extra nitrogen conversion "real estate" went away, and could be met simply with in tank or sump live rock.
This is not to say that they can't be used, only that technology has allowed us in many cases to leapfrog past that means of achieving the same end result.
Alternately, people developed a more effecient refugium technique, which used natural (as opposed to mechanical) means of nutrient export, which again allowed for the removal of the balls.
There is little documented evidence of bioballs being an actual hindrance, but by utilizing more modern techniques anecdotal evidence (in the form of low nitrates in systems lacking them) points to situations where they are not beneficial.
There are a lot of ways to lower nitrates... space, time, and budget will ultimately dictate the best way for your system to meet these goals.