Scarlet
"It's all Materia!!"
Rufus
"The ouside is rich with Mako energy, The inside is a treasure
trove of Materia. This truly is the Promised Land."
Hojo
"There is no such thing as the Promised Land. It's a legend... an
old wives tale... ...it's utterly ridiculous."
(The camera pans back down to show Hojo standing near Rufus. Rufus turns
to face him.)
It's clear from their reactions that the mako is so abundant inside the crater that it would be very profitable to exploit. Rufus even calls it "The Promised Land" his old man was seeking, the implication being that if the old President had known about this place, ShinRa's HQ would now be at the Northern Crater.They are not even particularly deep inside the crater at this point, and as others have pointed out, the crater is easy to access by air. If Jenova was found in the Crater under Shinra's aegis, then the only way Shinra could not know about the immense mako wealth inside the crater is if Gast/Hojo/the science department somehow found a way to keep this fact a secret. That's why I prefer to think that the reason they keep her in Nibleheim is because that's where they found her.