Welcome, zibnata and Achilles!
First, your observations of your animals are one of your best indicators of true health. If they're thriving, then I would look to anomalies/problems with the test kit itself. (In other words, if it ain't broke, don't fix it.) Your canister can either help or hurt, your animals are healthy so it can't be that bad. I also wouldn't simply get rid of the cc, but would put the new substrate in pantyhose and place where there's good circulation so it can become sufficiently seeded.
Second, the thing about bioballs being "nitrate factories" is at best a bit of a misnomer. As we look at the cycle of ammonia oxidation (nitrification) we see that there will only be enough end result (nitrate) as there was "food" to go into it in the first place. In other words, you will end up with significant nitrate readings because there were significant amounts of ammonia (due to many things--bioload, detritus, etc.) to begin with. If you address those start point nutrients, the end point becomes moot. I hope that made sense. Basically, it means that the bioballs are doing there job, which must be done. This is where something like foam fractionation makes a lot of sense.
Third, clams are actually helpful in "filtration" of nitrogenous compounds.
Fourth, if you have addressed initial nutrient export issues, a DSB and refugium would be my next suggestion. In my opinion, unless you're in a big hurry, there's no reason to lay out the cashola for live sand. Place it in the system and let it become seeded. I will very strongly push a 'fuge, actually, as you can get it going with macros, you will end up with a little "pod factory" that will feed your filter feeding wards quite well, and if it's going well enough you can get rid of the skimmer and the canister (should you wish). The point of removing those forms of filtration would be to preserve the microscopic life that would feed these filter feeding animals. Aragorn has had his reefs set up this way, practically from the beginning, and they are thriving as well.
In order for a deep sand be to denitrify it'll need to be sufficiently deep. Most agree that this means at least 3" (depending on grain size, of course). Based upon the experience of others/observations, I will suggest going with either a mix of sand and cc in the 1-2mm range, or entirely with the cc of that size, and making the bed deeper, on the order of 5"-6", to achieve sufficiently anaerobic areas.
HTH!