Anderton
<<Sonar is NOT re-enabling other things "silently and automagically" in general (f.e. Audio/MIDI inputs), so that can not be "by design" either.>>
Well azslow3 I don't have you blocked, so I can answer. 
Thanks! I have not blocked you, so we can continue the discussion
The reason why I think it is by design is because Noel said it was in his blog post on VST3 implementation (which actually contains a lot of useful information). He said:
Enhanced VST MIDI Out functionality
VST plugins that support VST MIDI out are directly supported without needing to register them as a synth first. A MIDI out port is enabled automatically when a VST plugin supports MIDI output.
May be for you (some other users here also claims so) this section of the blog is clear and strait. For me it is not.
Before I continue with the explanation, I want to add the next statement in the section, it can be relevant for the explanation:
A future update will allow MIDI input/output on such plugins to be toggled at will.
So, what for me makes that section "questionable"? The text I have marked bold.
Lets remember what was the subject of many questions in this forum, had the text I have marked as bold and WAS IMPLEMENTED in X3?
Was that questions about Audio->MIDI converters, presented themselves as FX? I do not remember many such discussions. What I remember are GuitarFX/Soft Pedal boards/etc., which are FXes but also have MIDI INPUT. To use them with MIDI input, users had to change the option in the plug-in manager to register them as "synth".
In X3 that was implemented. VST plug-ins that support VST MIDI
IN are directly supported without needing to register them as a synth first!
Was it a change which deserve a section in X2-X3 enhancements? I think yes. Do you see anything about it in the blog? I do not.
Now lets remember what was the change with VST MIDI OUTPUT between X2 and X3. The MIDI output was by default OFF and now by default ON. The users choice IS STILL NOT PERSISTENT. Does that deserve a separate section in the "enhancements"? Hm...
Then the quote I have added. CW was working with MIDI IN/OUTS, they have added input/output indication (and sometimes selection) to the "VST2/3" drop down menu. So they was touching the code also later. And it DOES mention that the user should be able to choose. There is NO explanation why the choice can not be persistent.
Also note that the whole change is NOT VST3 related, it was changed for all VST, including VST2. And I repeat, VST specification prescribe nothing about the use of inputs/outputs. VST3 has way more options to allow the plug-in EXPLAIN the host how it (plug-in) is using input/outputs. But still I do not see any words which describe how the host SHOULD use that information.
Now lets put all facts together:
1) in X3 was implemented many times requested feature to allow audio FXes also have MIDI
Inputs. Real requested enhancement. Yet that change is not mentioned in the blog.
2) in X3 the default, (still) not persistent after users explicit choice, setting for MIDI
Output is changed. And that change is represented as as separate section in the blog. Not as a "fix", not as "from users wishes", but as an enhancement.
That does not make sense for me.
And now my own SPECULATION: the blog has a typo! Replace "Output" with "Input", and everything makes perfect sense, including the text in bold!
May be Noel can comment who is right with the interpretation of his blog