With an IDE you're can just look at the class hierarchy/data types rather than the files. As long as those are well organized, who cares hoe they span files?

For instance, in C# a class can span multiple files using "partial" or you can have multiple classes in a single file. It's generally not an issue as long as the code itself is organized. The only downside is the reliance on an IDE, which is pretty standard these days anyway.