Yes and no. There is a convention of "hiding" files from being listed that begin with a period, and it is not builtin to the filesystem itself. The programmer gets to decide whether or not to follow this convention and how. Some programs make it optional and require that you specifically choose to show these files.
As for as FTP goes - regular FTP is not the same as using secure FTP (SFTP using SSH2). On DreamHost, if you use regular FTP, you have to configure your FTP client to use the switch that tells the FTP server to include the "hidden" files in a directory listing. I've observed that with SFTP these files are always listead.
For example, I am using CuteFTP Pro. It has a "Server-side filtering" setting that allows me to tell it use the command "LIST -a" instead of just "LIST". The "-a" is a switch that tells the FTP server to include the "hidden" files. But I don't need to set that if I use SFTP instead of FTP.
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