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.
As an attacker, you'd have some symbolic victory and maybe a few months of diminished function, but you'd also trigger a major military operation that would certainly destroy you. There's no upside.
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.