If we humans want to observe animals in the wild, what do we do? We build an outpost of some sort and camouflage it so it blends into it's environment without being noticeable.
The military take the exact same approach - bunker entrances and the like in jungles are covered with vine and leaves, those in the desert are sand-coloured, etc.
It stands to reason Kryptonians would have camouflaged their outposts in a similar way.
So .............. (and this may seem a silly suggestion) ............. why not have the Kryptonian fortress resemble a glacier. It could be as large as you envision it. By being exposed, it could remain solar-powered and have stored up hundreds - maybe thousands - of years of solar energy. And by taking the form of a glacier, it retains
some of the crystaline ice-hewn look of the original fortress.
A floating version (an iceberg) would be virtually inaccessible by foot, which would reduce the chance of it being found. Of course, for someone like Superman who can fly, it would make no difference. The picture below shows just how large a structure there could be under the water.
Most importantly, any travellers to the North or South pole would likely not cast a second glance at any glacier as they're so common.