Are there performance downsides while using autoloading classes in PHP?

This article has some information and benchmarks: PHP autoload performance (archived). Conclusion:

Autoloading does not significantly degrade performance. Include_path lookup, reading and parsing PHP scripts from disk takes much longer time than that bare autoloading logic costs.

Autoloading a class is almost as fast as including the class in the normal way. Switching to autoloading will improve performance in your case, because PHP loads less files and classes.