Real reason why Cloud's cell was mysteriously opened in the morning:
(SPOILER) Plot. If the cell hadn't been opened, Cloud and co. would've had no way to escape. They'd have died of boredom, starvation and Red XIII's B.O. in a matter of days. Not much of an ending to the game, really.

It's like the (FFVIII spoiler) inept Desert Prison guards in FFVIII who store the party's weapons only one floor above them in the cell block. If the weapons were safely secured in a locked locker ( tautology), along with Zell's lethal gloves, then the Squall and co. would be completely unarmed, and their grand escape would meet a swift and SeeDy end.

Plot considerations.
The best, the only way to escape the inescapable, survive the unsurvivable, and explain the inexplicable.