In practice in wordpress the number of SQL queries has the biggest impact on the performance of the site and the quality of the PHP code is usually irrelevant.
In theory for any additional PHP file that you include you delay your code by the time needed to fetch the file from the disk. This time can be small if the fike are memory mapped or big if it rund on an slow old harddisk. Therefor you should try to minimize the number of PHP files that you use.
The other factor is parsing. Before executing any file the PHP interpreter has to parse it, and if the file contain unused function then the parsing time was wasted.
Therefor the best approach to organizing your code is to have the core most used parts of it in one file and load other files only when needed.
But in practice anyone that cares about the execution speed on PHP level will use PHP code caching which if set correctly will cause that all php files will be read only once and all php code will be parsed only once.