It seems that the shell extension of the compressed folder ignores directories (but not files) whose names begin with a dot, unless explicitly specified as a parameter (that is, selected for the "Send" command).
It’s hard to know what else it excludes, since I can’t even find out what the first sendto element does, first of all, without reference to third-party documentation.
Edit:
OK, the sendto shortcut "Send to compressed folder" has the extension .ZFSendToTarget, which is processed by zipfldr.dll, which does all the work.
@Kibbee:
Mine includes hidden folders during zipping, although I have "show hidden files".
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