Why is the Pentagon not a giant honeypot / decoy? They paint a huge target on their back. You don't want to advertise your core infra somewhere obvious. You need your core infra in obscure locations where people don't look. Military strategy 101.
The Pentagon is full of think tanks and high level policy makers and paper pushers with command stripes all the way down to their pantlegs. They stuff they deal with is pretty much the military at its highest possible level of abstraction (though obviously also at its highest level of Intel clearance).
Any of the actual command and control rooms you are probably thinking of are much more likely to be buried under a mountain in Colorado somewhere or simply in the complexes of actual military bases than they are to be in the Pentagon itself.