Deja-dup is risking your security. Luckily the chances of an actual security violation occurring are low, but the possibility exists. Deja-dup backs up your files once they are unencrypted and then re-encrypts them with another kind of encryption.
You will have two copies of the same data in different encryption. Knowing this, a cryptoanalyst could use sophisticated pattern analysis to compare the two copies and find out what they are -- bypassing the encryption of both.
Another possibility is that one of the two encryptions may be weaker, even weak enough to partially reveal the content of your data, giving a cryptoanalyst clues to decrypt both copies.
It's even more unlikely, but an infiltrator could modify your local copy of Deja-dup to transmit the unencrypted data before re-encrypting it.
Backintime can be configured to back up your encrypted home directory as-is, from /home/.ecryptfs/user without even knowing what it's backing up.