Yeah no, literally burying your air assets with limited exits is not a smart move.
Let's say you want to disable a traditional airbase. Depending on your attack vector, you would first disable air defence and/or the runways. Additional soft spots would be munition depots, and C&C infrastructure. Individual aircraft wouldn't be high on your list if they are spread around the field in their individual hangars. It wouldn't make sense to go after them one by one at the initial phase unless you are carpet bombing the entire base.
Meanwhile solutions to these attack vectors are also in place in an airbase. Hangars are CBRN protected and spread out. Dedicated CBRN personnel and equipment is available. Physically protected communication pathways exist (In Turkish FKM). C&C centers (SHM), fuel and munition depots are underground and have at least one backup. Mobile wireless communication infrastructure is in place. You have prefabricated runway sections for quick repairs. Plus you have your poor infantry soldiers collecting pine cones all day to have strong backs for fast runway cleanup (YAMAHA) and so on.
Basically you bunker up what you need to be bunkered up. But keep everything quick to access, repair, redundant and spread out to reduce the amount of damage a single hit can produce.
Now if you put all that in a mountain with limited entry/exit points. You are basically creating super soft points to just burry your entire force with a single strike. Not to mention your runways will still be out there unless you build some runway in to the mountain a la James Bond. But even that would be disabled with a single slam dunk to the enterence.
Of course this doesn't mean we do not have facilities within the mountains. But those are generally for deep storage of explosive stuff.
But I agree we would need upgrades to our bases. I had a short tenure as part of support force within Eskisehir 1st AFB (just a soldier, Akın in MEBS) and eventhough F-4 hangars were lovely (cold war stuff with huge steel doors, heavy grandfather phones still on the walls and so on) at least their communication infrastructure needed a re-do. As a simple example or let's call it a cross section: I am assuming a simple analog phone line won't be enough for a 5th gen fighter's hangar. Probably a fiber link would be needed because these platforms would be fully integrated to HvBS and other mission/maintenance suites. Well, replacing a physically protected 1940s built copper line with fiber optic infrastructure which would have similar reliability is no easy task. You can't just twist two wires together to make 1 line have 2 phones in a modern network or run it with its power supplied only through the switchboard. Not to mention physically protected part of it. Just one very very specific example, but I think it gives an idea on how big the overall task is.
So there will be need for upgrades in our bases to support 5th gen of things, for sure. But they are combination of many many many subtle things. Not like throwing whole doctrine out of the window.