Running WPMU makes a big difference as the performance hit from one blog is exponentially raised as it's applied to a network of WPMU blogs ... so if your blog's slow down or spike is only 10% ... which is fine ... it affects my network over 300%, which is horrible.
Sorry, but that's total nonsense. You may have more hits, but this does not affect the percentage of performance impact of any given piece of code. You're not running 30 blogs. You're running one blog with 30 different viewpoints. That's the whole point of WPMU.
Regardless of whether or not the code is "used" it still has to be executed, which many PHP programmers know, often takes more time then the execution itself.
No, it does not have to be executed. It has to be parsed and compiled into intermediate code. While the most naive implementation would require some overhead for having the code in there, a more intelligent PHP processor, like Zend Optimizer or Alternative PHP Cache (APC) would actually cache the resulting intermediate code for later execution between client communication sessions. Implementing JIT compiling would be a good approach too, but I'm not aware of any PHP implementation that has done that yet.
Anyway, if the time compiling the PHP is your problem, then removing code isn't the solution. The solution is to make it stop compiling all the time. If you're running a large site, you really need to be using APC or one of the other PHP optimizers. Especially if CPU time is a big concern. APC is free. http://pecl.php.net/package/APC