Actually it made quiet some sense the heart wasn't in it.. it would have been stupid...
I mean... a whole Game and Province's History was centered around that thing.. and then it would have been implented as being locked in a frozen glacier in skyrim and only be sought by a crazy wizard?
Then again it would have made some sense for the Dwemer to have had a backup plan for if their enchantments broke or if there was a risk of the enemy obtaining it - what better place to send it than some random box in a glacier that nobody's gonna look in without being guided there by a Daedric Prince.
And still, what the hell was that box doing out there? Or better yet maybe the Heart was in there, but Herma Mora snatched it away as soon as the lock broke, giving you the book for your work. Probably not, but still.