I need some clarification on the performance of a website.
Assume server configuration is optimised and the same, just think about file size and number.
This is not something that can be answered with a yes or no. You would have to benchmark how many requests/second your application could handle to see. My opinion is that the difference is insignificant given a properly configured server.
If you use something like APC, the files get parsed once and stored into memory. At that point, the distribution of the lines of code is hardly relevant.
If you are not using something like APC, then you have two main things to consider:
File I/O time. Accessing multiple smaller files can be slower than accessing a large file.
Parsing time. Parsing a large file will take more time than a small one. If you are parsing more than you need, then you are wasting time.
But again, as most people will tell you, this is probably not something you need to worry about. And you definitely shouldn't worry about it if you cannot prove that it's a problem with benchmark and profiling tests.
If you are only "using" 50 lines out of a 10,000 line file, then yes you are losing some performance... in both speed for the PHP to parse the whole page even though it isn't using 9,950 lines of it - as well as "developer-hell" where the development time to find this function and understand that the other mountain of code isn't relevant.
That said, don't take a 10,000 line "utility" file, and split it into 500 separate files with 1 function in each of them... called randomly as needed (the opposite pain).
Well, here goes a clarification:
A code itself well be least thing to affect performance. And Assume server configuration is optimized
is just empty blab. It's endless process and depends on many factors.
If you want to optimize something, you have to run profiling tests first, then determine a bottleneck and then optimize it.
There are many opcode caching solutions that makes your question totally obsolete.
Listen to good advise, do not ask questions "in general". Especially such useless and imaginary ones.