File-paths in iCloud: Tilde ( ~ ) within the paths. What's the meaning? The tilde-character is a short-cut for the home-directory of the currently logged-in user (in UNIX-like operating systems).

In the paths of iCloud-directories it is included too. 

For example:

com~apple~CloudDocs


or 

com~apple~mail


What is it's meaning there?

And in general:
What's the reason for these weird file-paths?
The reason for naming things like that starting with top level domain and going down to being more and more specific is to have them grouped automatically when listing them. This is common practise for things like java classes or preference files (but usually separated by dots).

Using the tilde character has nothing to do with the home directory tilde. I guess it's just one of the last remaining symbols of the standard charset without a special meaning in this context, while .:;&lt;&gt;$/"*# and so on may have conflicts with different interpretations.