This depends on the threat scenario. Sure, in Belgium or the US you won't see defense factories going underground any time soon. But Poland? Doing so already proved a valuable investment for Iran - even facing an enemy with an abundance of fancy bunker busters. Ukraine also started to build energy infrastructure and weapon production sites underground, and even Russia finally started building protected shelters for their military aircraft. I am pretty sure the US will also reconsider their arrogant assumptions of high tech superiority going forward, when it comes to their bases in the middle east, where they got very, very expensive stuff destroyed by Shaheds oversaturating Patriot systems. You see, deep underground cities and bunkers withstanding nuclear strikes are not required. You only need a bit of concrete and dirt to withstand medium yield flying bombs arriving with low kinetic energy (unlike ballistic missiles). Hobbit style housing. A cheap drone will never be able to dig itself into its target, since cheap and fast are incompatible.

That said, of course some important components can't really be protected passively. E.g. comms and sigint will always have expensive, hard to replace antenna arrays exposed. But narrowing vulnerability down to those assets means you can focus scalable air defense and EW measures there.

Again, this benefits the country on the defense, especially against distant enemies, since you can build bunkers etc. at home, but can't really bring them along. And bunkers are one time investments, theoretically good for centuries (WWII/Soviet bunkers are still all over the place in Europe). I think, it would be viable for a peaceful country to almost entirely invest military funds in bunkers, drones, drone comms and crews/AI, and possibly nukes, to discourage any aggressor, while minimizing peacetime running costs . Additionally, highly decentralized renewable energy like solar and wind makes that sectors really hard to disrupt. Especially individual solar installations, battery storage and electric cars potentially enables quasi autarky for large portions of the population. Mighty "petrol station" Russia, got fucked by their reliance on ICE. Solar and wind will work even in nuclear wastelands, and replacing that solar panel is still cheaper than the cheap drone, which damaged it.

Tl;dr: You can restructure military doctrine and defense focus to make bunkers an easy sell to your citizens. In fact, going any other way should raise questions about aggressive ambitions.