I really don't see that as a problem. Having transperancy of the money supply is one of the most important things that make Bitcoin special. Think about it - you can never really know how much gold or dollars there actually are in the world. You can have an estimate, but not an exact value like in bitcoin. CoinJoin solves the issue of fungibility. You can't claim for sure who owns the coin joined bitcoin. And if enough people used wallets that have coinjoin then bitcoin becomes even more fungible. This is a good way of doing it as it's an "optional" feature keeping the base layer as pure, generic and effective as possible allowing things to be built on top of it. And, perhaps one might argue the lightning already improves the fungibility of bitcoin by a large factor.