Yes, every include makes your program slower, but there is more to it than that.
If you decompose your program, over many files, there is a point where you're including/parsing/executing the least amount of code, vs the overhead of including all those files.
Furthermore, having lots of files with little code ain't so bad, because, as you said, using things like eAccelerator, or APC, is a trivial way to get a crap ton of performance back. At the same time you get, if you believe in them, all the wonderful benefits of having and Object Oriented code base.
Also, slow on a per request basis != not scalable.
As requested, PHP is still faster at straight up array manipulation than it is classes. I vaguely remember the doctrine ORM project, and someone comparing hydration of arrays versus objects, and the arrays came out faster. It's not an order of magnitude, it is noticable, however -- this is in french, but the code and results are completely understandable.. Just a note, that doctrine uses magic methods __get, and __set a lot, and these are also slower than an explicit variable access, part of doctrine's object hydration slowness could be attributed to that, so I would treat it as a worst case scenario. Lastly, even if you're using arrays, if you have to do a lot of moving around in memory, or tonnes of tests, such as isset, or functions like 'in_array' (it's order N), you'll screw the performance benefits. Also remember that objects are just arrays underneath, the interpreter just treats them as a special. I would, personally, favour better code than a small performance increase, you'll get more benefit from having smarter algorithms.