Like the title says…VST3 version of Amplitube 4 can not be bypassed from the mixer. You have to open the plugin’s GUI and do it from there. The VST2 version of the plugin works fine.
I am seeing this as well. I submitted a ticket to IK Multimedia.
IK know about this as I contacted IK support the day after A4 came out. I have found that A3 vst3 works fine otherwise. I am sure there will be an update soon. I haven’t tried 4.0.2.
Indeed, they just sent me a response to the ticket I opened:
Hello,
Thank you for your email.
We appreciate your interest in our products.
At this time, our development team is aware of this and working on a fix for this issue. Be sure to keep an eye out on the IK Multimedia web site for updates to AmpliTube.
I’m fine with using the VST2 version until a fix is in place. 
Stutteredit seems to have the same problem, based on a very quick tryout here.
There is quiet a few plugins that do this, they do not BYPASS, you have to shut them off.