Note that they are not saying they are not deleting the encrypted message contents too. What they are saying simply indicates that what they promise is that they delete the keys.
There are practical reasons to do it this way: You only need to ensure that you delete one key per user (you keep a "current" key, that is anything up to two days old, and a previous key that you delete once it reaches two days), vs. deleting a possibly much larger amount of data entries that might also be more likely to be cached all over the place.
If I were to design a system like that, I'd try to delete the contents, but assume that I'd miss something, and aim to delete the keys too. I'd probably also make at least portion of the key depend on a site-specific set of secret rolling over with time that it should be policy not to log etc. to make it even less likely that the full key would survive longer than it should.