Yes and no... It's a bit complicated.
The short answer is no. The DOT sticker on the side of the RV does not change. So, from a technical standpoint, the heavier axles (higher UVW) and a fixed weight rating (GVWR) means you have less "official" cargo capacity. The Independent suspension adds approximately 300 lbs per axle. We're not sure what's involved with getting the DOT sticker updated, but knowing government bureaucracy, it's likely not a simple process.
That's the "official" answer. However, on the real-life practical side, the answer is sort of. 
In reality, this added weight means nothing in terms of the actual capacity of the RV since it is the foundation of the RV itself adding the weight. In fact, I’d bet the actual capacity is increased by an amount at least as large as the increase in axle weight, maybe more. But, this is just an opinion based on some common sense. The only things really affected by the added weight are the tires. So, that is something to keep in mind.
For our personal setup, each of our axles (including the tires) are rated at 7K. That's 21K of capacity for a 20K RV. And, considering only 75-80% of the RV's weight rides on the axles, we have a lot more capacity than we need. Thus, our official unofficial opinion is that we're considering the extra weight to be neutral.
This is just our personal take. The added weight of the IS is certainly something to consider if you're not comfortable padding your numbers a bit in a very unofficial fashion.