A CVO is not a "rare" bike, regardless of model. While fewer of one given model or color might make it seem like it should be rare, they made fewer of that model/color because they don't sell as well as another model/color. As a percent of MSRP, they depreciate just like most any other Harley, with rare exceptions. Doing something like putting a different exhaust on the bike certainly will not make it worth less. Now changing tins, painting, or radically altering the "look" of the bike is a different story, if you're concerned about resale values.
The cash cows for the MOCO for several years have been baggers of one description or another. The "naked" bikes have been slower to move for years. Not taking anything away from a "naked" bike, but that's just a fact. I've seen CVO models like a Dyna, Springer, etc. sit on a dealer floor for months at a time. You rarely see that happen with a bagger. It's just the market.
Do whatever you want to do with the exhaust, but if you do more than slip on mufflers, you'll need to think about a tuner as well. IMO.