I really am not trying to fan the flames of this thread but some more background to answer some of your questions Sunchaser;
My wife and I boarded the California Zephyr in Sacramento on May 3rd of this year. Our destination of Mt. Pleasant does not have checked baggage. Anyone who boarded in Sacramento found the luggage racks in our sleeper packed beyond capacity. Therefore all sleeper passengers who had luggage were directed to put them in the un-occupied H-room. My wife and I waited for all passengers boarding to go first. I find life much easier to be patient. When I placed our bags in the H-room, it was VERY full. Also, we have the Amtrak paper tags, our Select luggage tags from the last few years as well as our own personal luggage tags. We are identified no less than five times per bag! We had everything we needed for the two day trip in our "room" bag, so there was no need to even think about our bags in the H-room. I have pictures of the procedings from what I saw on the platform and later from our sleeper room window when they were calling it a day. I am subject to random drug testing from my present employer. I would never risk the welfare of my family, so ingesting illegal substances are out of the question. That being said, I still want to be present if my property is searched. I have my reasons that I won't go into here. And lastly, my Iowa drivers license has all the information needed to prove my citizenship. My name and birthdate gives them all they really could need. But the kicker is the magnetic strip found on the back of my license. All they have to do is swipe it and there is more info there than even I am aware of! Peace!
I can explain to you why the bags were searched. This is based on the case files I have read where people transporting narcotics were arrested in similar sweeps on Amtrak, I also have read a few files where people were caught transporting drugs on Greyhound as well. Even if the bags have tags on them with your name and address because they are not with you, meaning with your person or in your presence. Here as you presented the fact that the luggage was located in the "H" room and not in your room which to them (and they would act similarly if the bag was located in the lower level rack not just the "H" room) means the bag is unattended.
Now, I totally understand why you would want to be present if your property is searched. That said, if the agent had a manifest they should have located you, asked you if that was your luggage and asked for consent to search. Even without a manifest they still should have asked the people in the car if they had luggage down in the "H" room and if so which bags belonged to them and ask for consent to search. It makes for better public relations.
For clarification, when the sweep was conducted did the agents come to the upper level of the car and start ask questions of any of the passengers there? It was not stated in your original post and gives me more room to better analyze the actions of the agents.