FTP limit

[kobra]

I have a product catalog over roughly 9000 and a large image directory.

Would have been better if you had checked the limit earlier
Try placing them into sub-folders inside of /images

This also keeps them from showing up on my website.

I am aware that you will not see them in FTP but are you sure that they are not displaying?

[kiddo]

Yes, HM will limit the number of rows returned with FTP. (most hosts do)

If you use ssh (sftp) program like WinSCP, there is no limit and you will see all your files. Plus, it is much more secure.