It's not that simple. You just need to sit in a programming meeting with a client (like the institution you're taking about) to realize the trickle-down effect of trying to make such design decisions.
I'm not saying there's a "better" solution to having the racks hidden away, but the idea that it's "simple" is false.
Not only that, but I've had experience on large college campuses where the bike racks are out in the open with parts and bikes being stolen or damaged in full light of day and with people all around. Short of posting a guard, you're not going to be 100% secure (and even with a guard I wouldn't expect security).