For a directory on my website I only see 3000 files through an ftp-lister.
Checking online I see there are more then 4000.
Does DO limit the number of files?
And how can I change this?
I already got angry at my hoster because they reported more space used then I could see myself! 
Have you tried using another FTP client?
Is there any pattern behind which files are hidden?
I've used Opus on folders with 300,000 files in them. I'm not sure what the biggest number of files I've seen in an FTP or SFTP folder is but I'd be surprised if there is a 3,000 file limit coming from Opus itself.
Thanks Leo,
The problem seems to be a setting at the server. Mosts servers show maximum 2000, mine 3000. Solution is to use submaps.
Just got this reply from my hoster.