Bio Balls are a great media for a wet dry filter, as they allow air to flow into the balls quite well increasing oxygen exchange...
But as for submerged media, the open space within the balls is simply wasted space. There are many other medias that have far more 'surface area' than bioballs (such as ceramic rings, pot scrubbies, etc). This surface area is what bacteria need to live on...
In my experience, it is very very rare for "not enough surface area" to be the cause of ammonina/nitrite in the water... Much more common causes are overfeeding. This usually results in spikes of ammonia and the bacterial colony cannot grow as fast as the ammonia rises, then when the ammonia is gone the 'extra' bacteria starves off thus allowing the next overfeeding to cause another spike.
The other common cause is increasing the stock on a tank too fast. It sounds like this system has been established for quite some time. Can you confirm/deny this? In other words, how long has this set up been set up and stocked?
In all practical terms, it wouldn;t really matter if you had more water hit the bio balls for less time... or less water for more time... as there is ammonia equally in all fo the water that is not being processed.