PHP - SQLite vs SQLite3
SQLite2 internally stores every value as a string, regardless of its type.
Upgrading to SQLite3 will certainly shrink the database size since numbers and BLOBS get stored in their native formats, which could make things run faster.
Another big advantage in my opinion is that recent versions of sqlite, (starting from 3.6.23) support foreign keys.
Since you were using PHP, I would suggest that you look into PDO. It could prove helpful in case you need to change the DBMS for the application
This documents from the sqlite.org website: http://www.sqlite.org/version3.html it doesn't talk about performance, but differences. anyway there are not update to sqlite2 I personally recommend using latest and greatest version 3 (see Improved Concurrency, always good for web applications).