The commander requires line of sight, so no reason to imagine it might work through the umbrella. However, it probably is no problem, because the flash is probably situated somewhat to the side, and line of sight is probably possible, at least in most reasonable situations. I never have issues with it in umbrellas.
See this:
Using the Nikon CLS Remote Wireless Flash System
That was an intentionally silly setup to show the automation, but this line of sight concept is not far off. A couple more examples above it on page.
The flash head rotates on the body, so the body can be positioned to aim the side sensor at the camera, and still aim the head into the umbrella. If you can do that, it will work, at least indoors. And in truth, if the camera is close, say within maybe 5 feet of flash, it will work anyway, even if the flash is behind the camera.
See
Mounting Speedights in Umbrellas about first tries with the umbrella mount.