The mission owner (which should be the same as the TB owner) will get an email for every log posted at Project-GC on the mission. It's not very well tested, so if that doesn't seem to be the case, we are interested to hear about it. But I posted a note on a rescue mission today, and the mission owner responded within 1 hour. I assume that proves that it works.
I personally believe you are being helpful when posting notes on the rescue mission when there is information to be shared. I believe it's better suited on the rescue mission than on the trackable page at Geocaching.com.
The downside is that it's less likely that someone will actually go check the geocache for it. I would be more reluctant at least. I rather go check for a trackable that I believe is there, than one that most likely isn't. But with time, I guess someone will. Regardless it's very likely that it's gone anyway.
I also believe that since this is quite new now, owners of trackables have added missions for trackables which they are quite sure are gone. They want to test the system, and maybe increase the site stats, and their own. With time, I assume this will be a lesser problem.
I hope I didn't miss answering any questions, I only saw one, the rest felt more like statements and a discussion (which is certainly fine).
As a side-note. We have had some contact with Sasha as well. Before we had our first version out, he gave us some basic thoughts. We had actually already thought about it all, but he really tried to be helpful. Much appreciated from our side, and I assume the community is thankful for it as well.