You're worrying too much about something that doesn't mean much. WordPress doesn't care how many PHP files you have; the PHP interpreter does. And the PHP interpreter really doesn't care about the number of files until it *actually accesses those files and executes the code*.

Modern servers and PHP are so fast that you're not going to see an appreciable difference in the speed that the interpreter reads files. With 10,000 files, maybe there will be a slowdown. But that's more the server, the storage (HD or SSD), RAM, etc., dealing with the files themselves and not the PHP code in each file.

Now, *what is in those PHP files will make the difference*. If you're calling the database with complex queries and calling external resources, than yes, a plugin will be slow, even with only one PHP file. The PHP code is the issue, not the raw number of PHP files.