That's just an extra convinience feature you can turn on or off, and doesn't have anything to do with whether the editor is WYSIWYG or not.
It's not like the program forces you to see red swiggly lines underneath words when editing...
>Hyperlinks are usually hit and miss; sometimes they print as 'blue and underline' (but, of course, are useless), sometimes they don't.
Which is configurable too in all editors I know of. And the "blue and underline" is not exactly useless -- it conveys the information that this part of the document was a hyperlink initially.
>In short, what you see is certainly not what you get
No, it's 99.9% of what you get, minus additional layers of information that people expect to be there, and you can turn on or off.
Previously I have used Xinha, FSCKEditor and similar, but there was always some problem with the resulting markup. WymEditor copes much better in this regard... (not affiliated, just really like the concept and WymEditor)
If WYSIWYG editing is not inherently limited, why do pretty much no editors actually support it? For example, spelling/grammar checkers are useful, but when pseudo-WYSIWYG editors implement them, they underline the text, or change its colour. This colouring and formatting doesn't appear when the document is printed. Hyperlinks are usually hit and miss; sometimes they print as 'blue and underline' (but, of course, are useless), sometimes they don't. Annotations don't print, but they do show on the screen. Automatically-generated content like page numbers are often shown differently, eg. with a grey background. Again, this doesn't appear when printed.
In short, what you see is certainly not what you get; but removing these non-WYSIWYG features would be a step backwards.