I have compiled ardour 2.7 on ubuntu and 64studio. I believe that it is a bug: when bypass a plugin, and then saves the session, it turns as active when load the saved session.
The same problem in ubuntu (compiled for 32 bits) and 64studio (compiled for 64 bits)
I can confirm this. An old session suddenly sounded strange, and on inspection a number of bypassed plugs were active again. I removed the problematic plugs, and all was well. I suppose it is better to remove the plugs rather than have them in there and bypassed.
It could be a bug, but it might just be a reminder to remove unneeded stuff from your session.