I think it's a LOT slower. I haven't done tests myself but I've read of people gaining massive speed-ups by combining many small include files into one big chunk. PHP code parsing is lightning fast compared to file access. But as you said, with a good opcode cache the problem might not exist at all. It also depends on the efficiency of file caching by the OS - when I start a php site on localhost that has lots of includes I have to wait a few seconds hearing disk thrashing but after that the files are grabbed from a memory cache and the slowness almost disappears.
- for example, is including a hundred 10k files really slower than including one 1,000k file?