Yeah, personally I'd prefer it to have always been uninhabited, but the rock formations were designed that way deliberately. If a future story wants to reveal LV-426 once was, in ancient times, an inhabited world which was reduced to a hive-covered Lovecraftian horror, I'd be fine with that.
I don't think Hadley's Hope would have necessarily uncovered anything, though. That would assume something was exactly underneath them. If there waere, say, an ancient network of tunnels, they would have probably just registered as natural caverns.
I always go back to how, technically, the egg chamber measurements have no way to fit inside what we saw of the derelict's hull. It's actually more plausible to interpret that scene as O'Bannon intended: It's somewhere the derelict docked to, possibly hollowed out by an even more ancient civilisation. I always found it intriguing that the chamber gives the impression of going on for possibly miles around that corner.
If someone were to start excavating beneath LV-426, who knows what they might find if they looked in the right place?