I'm using Poco 1.4.2p1 with my own SEE-like implementation of Sqlite 3.7.8 and 3.7.9 with no problems.
But I had to add a few lines of code to Poco::Data::SessionImpl in order to have SessionPool utilize encryption/decryption capable version.
Another alternative is to pass the "PRAGMA KEY=" for each new connection to avoid modifying Poco.
Yet another way might be to have your own SQLite::Connector and call its registerConnector();
It seems sqlite3 files distributed with Poco is unmodified, so I simply replace them with the latest plus encryption code.