Does Network Link Conditioner Work Well on El Capitan
Yes, It will perform as expected.

Bear in mind that the Network Link Conditioner has noting to do with Xcode itself, but with the OS. 

When downloading theses Hardware tools Apple points out that these graphics tools support running on [OS] which might lead you to think that and update is necessary, but the protocols and / or the way the NLC interacts with the System's connectivity, doesn't seem to have changed, as it does, indeed, work.