I believe, there is no functional difference between FTP and HTTP site.
It depends on environment. In some environments, customer doesn't use HTTP so in that case, they can opt for FTP and vice versa.
My personal experience in our organization that NaiFTP is a bit slower than NaiHTTP.
For example when doing master repo pull task.
And I believe you'll see more data transfer required for FTP updating vs HTTP as FTP updating constantly needs to create new connections. Not a huge amount more, but it could cause issues in some environments.
At my org, I do a HTTP pull, replicate, and then an FTP pull, replicate about 15 mins later. I have experienced issues with one type of update site at times, so it's a backup.