I would advise against un-ticking 'Organize Media' unless in a situation where you are handling storage elsewhere.
Having a large amount of files in one directory is flawed for many reasons, though there is some situations where this is unavoidable but for a website this is always unavoidable.
I inherited a Wordpress website and was tasked with moving it to another host. This proved to be a problem since all uploads were in one folder, over 93,000 files - yes 93 thousand.
No FTP client was able to index that many files and simply would not navigate into the folder.
I had no shell access to the system.
I couldn't do a full dump using the hosting control panel as there was no option to do so.
I had to rely on the hosting company to do a dump for me, which was a task in itself tying to get them to do it.
Apart from these potential issues, indexing thousands of files is slower than indexing tens or hundreds of files - simply, performance is effected with large amounts of files in one directory.