This is MIDI *output* not MIDI input btw. We don't enable MIDI input by default. 
Are you seeing a lot of plugins that are showing up this way? Are they VST3 or VST2?
I also just fixed a bug where the scanner was erronously flagging some plugins as having MIDI output so its possible that you ran into that. However I only saw this on some Waves plugins bit not other stuff.

Noel Borthwick [Cakewalk]
This is MIDI *output* not MIDI input btw. We don't enable MIDI input by default. 

My bad. But effects with MIDI output are even more rare, aren't they? Aside form pitch correction and drum replacement effects, I can't think of any offhand. Due to the ubiquity of Komplete, I'd imagine the incidence of false positives will be about as high as the incidence of real positives. Is an opt-out approach really preferable to an opt-in?
 

Noel Borthwick [Cakewalk]
Are you seeing a lot of plugins that are showing up this way? Are they VST3 or VST2?

Both the Plug&Mix effects and the Komplete effects are VST2. If you've got a loose build of the new scanner handy, I'd be happy to give it a whirl tonight.

FWIW, this issue still occurs in X2B. I do not see a way to manually tell Sonar that these plugins don't have MIDI outputs.
 

Noel Borthwick [Cakewalk]
I also just fixed a bug where the scanner was erronously flagging some plugins as having MIDI output so its possible that you ran into that. However I only saw this on some Waves plugins bit not other stuff.

Doesn't look like the same bug, then.

The manual config for this isn't in X2B. Possibly the next update..

I'm not sure that this is really answered.
 
I also have this issue with the Native Instrument solid and vintage compressors.  I just looked at the manuals for a couple of them and found no mention of midi output, in fact the word midi doesn't appear anywhere in the manual.  I can't see why a compressor would produce midi output (but anything is possible).
 
If I load an X2 project that has an NI compressor into X3, it does not show up in the synth rack, and the effect works as expected. These are VST2 effects, and they are not configured as instruments, in X1, X2 or X3.
 
I created a bug a report and was told that I should contact support because it is a configuration problem.  Still misbehaves in X3B.
 
Jim

Installing X3b patch - I went and checked rescan of existing plugins and scanned - all my VST3 effects stuff suddenly became listed among synths, and none among effects.
 
I also checked plugin manager and synth was checked. I don't know if this was about the Waves shell or something.
 
Making a reset, then scan fixed that again back to how it was.
 
So if making rescan of existing strange things might happend.

Found another effect that appears in the synth rack: The popular free TDR Feedback Compressor. Interestingly, Version 2 of the same compressor does not appear in the synth rack.