Website Content Management Systems (CMS) including the most popular; WordPress use a set folder structure, very similar to a windows computer (My Computer > C: > Users > your name > Documents > and so on….) which keeps files and code organized for future changes and enabling servers hosting your site to optimize the performance of your site.
Developers and designers can still create and manipulate content for your desired look and configuration while maintaining a standard and organized folder structure.
We have experienced previous developers to websites we have taken over created their own folder structure and storing functioning scripts & media (images) within folders on the root of the website, using the windows comparison again; this would be the equivalent of saving all your pictures, music and Documents to My Computer and not within the designated folders within my Documents.
This does not necessarily affect the performance of the site (using box standard hosting) however the following potentially could be:
If the standard folder formation has not been used and someone compromises the site and uploads a malicious script this would unlikely be detected, as the foreign code could hide within the unrecognized data structure which in the long run could severely damage the site as Google would penalize the site for being malicious.
If you wish to update the code or content, it may not be simple as it should be due to the content is not following the ordinary CMS / WordPress / Joomla structure, especially if using a different developer/designer that created the site.
Specialist servers which have been streamlined and optimized for specific CMS websites such as WordPress will not be able to operate as designed because the server will be looking in the wrong location for certain data.
Make sure your designer and developers have filed your website contents accordingly, if they haven’t liaise with them in remapping the contents as per the normal structure for your website system; if not you could encounter some serious problems especially if you change your website designer/developer, as they will have to unravel and remap your website code which in some cases can take as much time as creating your site from scratch.