if you have enough flow then the bio balls will still be doing what they would if they were in a filter. with enough flow water will be circulated around the balls, almost like a filter. everything that the water touches, rocks/gravel/sand/wood, in your tank has beneficial bacteria on it so basically your tank is one big bio filter.
they will probably make your tank a bit less pleasing to the eye though.
bio balls are, in fact, an effective media in almost any type of filter and are far from useless as is mentioned above. they may be more efficient in a wet/dry but they certainly arent useless.