Transparently encrypted storage of *any* kind (storage engine based data encryption, truecrypt volume encryption, bitkeeper, etc) is *just as insecure* to most types of attack as non-encrypted data.  SQL injection or security escalation vulnerabilities, operating system vulnerabilities and cross site scripting attacks could give attackers access to the database data.  It doesn't matter if you encrypt the database's physical storage in the database itself (in the storage engine layer) or on disk (at the filesystem level) since either way the data is presented unencrypted through the SQL interface. 

Transparent encryption is great for protecting your laptop data from theft by stealing your laptop.  It is very unlikely someone will attack your server by stealing it.

It doesn't protect you from a malicious SQL injection which drops all your tables or reads all your data.

If you are …

Transparently encrypted storage of *any* kind (storage engine based data encryption, truecrypt volume encryption, bitkeeper, etc) is *just as insecure* to most types of attack as non-encrypted data.  SQL injection or security escalation vulnerabilities, operating system vulnerabilities and cross site scripting attacks could give attackers access to the database data.  It doesn't matter if you encrypt the database's physical storage in the database itself (in the storage engine layer) or on disk (at the filesystem level) since either way the data is presented unencrypted through the SQL interface. 

Transparent encryption is great for protecting your laptop data from theft by stealing your laptop.  It is very unlikely someone will attack your server by stealing it.

It doesn't protect you from a malicious SQL injection which drops all your tables or reads all your data.

If you are …