There are a couple conflicting parts here. The comment about being able to do whatever you want is true, but it will also make much more work for you in the long run.
If you have any idea about re-arranging anything outside of your home directory, stop! That's way more complicated than you think and you should leave it alone. If you don't like it you should change to a different distro or even operating system. If none suit you you would need to roll your own, but you can't just move system directories around without getting burned. See this question for some idea what would happen if you wanted to go that way.
So we're down to your home directory.
First of all, remember as you think up a structure that permissions are hierarchical. In order for somebody to have permissions on a given folder, they need to have at least execute permissions on every folder ABOVE that folder. If you have anything in your home directory that you share, it needs to be near the top (e.g. ~/Music), anything you want to restrict should be in subfolders with limited permissions (e.g. ~/.ssh/id_rsa).
Secondly, there are no rules or even best practices per-se but there are conventions. Lots of software use default values that you may or may not be able to change, but even when you can change them it's troublesome to have to do constantly. Gnome, and particularly Ubuntu stuff, likes folders with nice names starting with capitals. If you try moving "Downloads" to "downloads" you'll find the original probably gets created again before too long by some program with an assumed default. You'll have to decide how much swimming against the tide you want to do in these cases.
People say you shouldn't spaces in Unix file naming.
People say a lot of things. There are some tools that may screw up, but hopefully they are few in number at this point in time, since spaces are a virus proliferated by giant consumer proprietary OS corporations and now impossible to avoid.
Spaces make specifying filenames on the command line, etc., awkward. That's about it. The only categorically prohibited characters on *nix systems are NUL (don't worry, it's not on your keyboard, or anyone else's) and /, since that is the path separator.1 Other than that anything goes. Individual path elements (file names) are limited to 255 bytes (a possible complication if you are using extended character sets) and complete paths to 4 KiB.
Or is this just a matter of personal preference
I would say it is. Most DE's seem to create a slew of capitalized directories in your $HOME (Downloads, Desktop, Documents -- the D is very popular), so there's nothing bizarre about it. There are also very commonplace traditional files with capitals in them, such as .Xclients and .Xauthority.
A value of capitalizing things at the beginning is that when listed lexicographically they'll come before lower case things -- at least, with many tools, and subject to locale.
I'm a fan of camel case (aka. camelCase) and use it with filenames, e.g., /home/goldilocks/blueSuedeShoes -- never mind what's in there. Definitely a matter of personal preference but it has yet to cause me grief.
Java class files tend to contain capitals by nature, because Java class names do. And of course, let's not forget NetworkManager, even if some of us would prefer to.
1. There is a much more delimited, recommended by POSIX "Portable Filename Character Set" that doesn't include the space -- but it does include upper case! POSIX also specifies the more general restriction regarding "the slash character and the null byte" elsewhere in the same document. This reflects, or is reflected in, long standing conventional practices.
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