While it is disappointing that Skyhold isn't ever used for a siege event or something, it's kinda not surprising.
I mean, have you seen it?! The place is so ridiculously defensible it makes Helm's Deep look like a fucking Walmart or something.
It's on top of some ridiculously high ass mountains and has huge drop offs on all sides, and there is only one single fucking point of approach on a slim ass bridge. How on earth would anything other than a couple dragons be a threat to this joint? The entire Orlesian, Fereldan, Qunari, and whatever else armies could all march up and get fucked cus they'd have to hike up these mountains and go across this bridge in like lines of 3 lol
You siege Skyhold you get massacred