Force simple UNIX path names for optimal us of command line apps?
Unfortunately, you just have to remember to do it each time you make a file or directory. There's no way you can do this via software tools or by formatting to a particular file system. After the fact you can use software to convert spaces to '.' or '-' however.

Obviously what you describe is an excellent idea and good practice when working in a *nix environment. You'll probably find that the more time you spend in the Terminal, the more inclined you'll be to create short, non-spaced file names. Unfortunately Apple themselves make your task an impossible one in that they often use multi-word file or directory names.

As to the first part of your question: You can be sure that you'll always be able to manipulate files in the Terminal, even if they contain many spaces, etc. It's just a case of 'escaping' the spaces by typing a '\ ' where the space would be, as you point out.

Tab-completion can be a real time saver here, but it's generally better to avoid the problem in the first place.