The downside is that a single request have to touch a lot of PHP files, sometimes up to several hundred. In the "bad old days", each file must be read from the disk, parsed into byte code and executed by the PHP interpreter if byte code caches like APC wasn't installed. That took a lot of time and PHP applications could require up to several seconds to finish a request.
Since PHP 5.5, performance improved very much, mostly by the integrated OPcode cache, since PHP7 also by various optimizations inside the PHP interpreter itself. Now, request times of even big PHP applications can be only several 100ms or below. PHP applications can be almost as fast as Java one. Great stuff!