In PHP 5.4 sqlite got moved to PECL. In order to use the old sqlite API in PHP, a dev-php/pecl-sqlite would be needed. NEWS file mentioning the change: http://www.php.net/releases/NEWS_5_4_0_alpha1.txt
SQLite has not had a release since 2004. It does not work with php 5.4 yet.
When upgrading from PHP 5.3 to PHP 5.4 it can easily go unnoticed that sqlite support is removed. To help avoid this pitfall, maybe the "sqlite" use flag for dev-lang/php should be restored for the time being or renamed to "pecl_sqlite". The use flag should draw in the new dev-php/pecl-sqlite ebuild as a dependency.
Closing this issue as wontfix since Gentoo is moving towards dropping sqlite2. See bug 249418