I understand there is a need of placing different categories of resources in separate folders for the sake of organization. But is there any noticeable decrease in page load speeds accompanied with it that adds up as you add more and more folders or go deeper folder within folder and so on?
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No. The HTTP requests are a few bytes larger because the URI is longer, but that's negligible. But it shouldn't matter whether the file is 1 directory deep or 30 directories deep. AFAIK, it's a bigger problem when a single directory contains large numbers of files in it.