NetGuard can not see any Apps in the workspace. I tried cloning NetGuard to the second workspace, but I had to disable the first one to get the second running at all.
For me this is not true. I am running WA within the work profile over shelter on my FP3, cloned NetGuard into the work profile and turned NetGuard on in both (so you have 2 NetGuard-Icons in the status bar, hmm). It seems to work as expected.