My personal experience with bioballs, both FOWLR and now reef makes me suggest keeping them if you have a decent number of fish. They do have a substantial surface area and will do a lot of work for you in cleaning up the water. Definately don't leave that area empty if you do go ahead and remove the bioballs-do something with it such as LR and/or a macroalgae. Maybe make a divider so you have both in your sump? I have a small pert of my sump (where the lousy built in skimmer used to be) that I have chaeto in.
I don't know about reducing the number of bioballs-if you do keep them, just clean them once in awhile and run with them! I clean mine evry couple of months or so and it's not such a big deal-I dump them in a bucket of water I have drained out during one of my regular water changes, swish them around to remove any crud, then put 'em back in.
With bioballs and other wet/dry filtration methods, as well as using macroalgae, you still need to be religious about doing regular water changes. My personal schedule is 20% every 2 weeks. Some do more, some do less.