Being in different folders or in the same folder will have absolutely zero affect on the time to load a page!!!

Organising your work by topic into folders will make it easier to find things, and given the number of files and sections you have, you should have done this a long time ago. Being properly organised really helps. That's why everyone with at least half a brain puts their images in one folder, JS/Jquery scripts in another, and leaves the basic hmtl in the root. so you may also want to consider where the images go - all in one folder, or an images folder within each topic folder? Perhaps the common images used in every section should be in one folder, to avoid duplication, and then the section specific images as sub folders within each section. Probably ditto for JS scripts