The cases more to the bottom are cleaned better in my experience. Makes sense, more waves to bounce around. Often times when I overload the machines, the top ones are rarely cleaned as well as the bottom ones (and the ones poking out from the top that are not dissolved get funny patterns on the brass that don't affect their performance, too!). The fill level advice isn't for safety as it is for efficacy.
Also, the machines tend to cannabalise themselves if loaded often or improperly. The ones in one of my bigger labs were used so often that they would stop being as efficient 1 year down the line. And these were $4k machines and not the $200 ones we find on ebay or amazon.
The bottom stains on the brass cases are often a mix of pyrolytic tars (think asphalt but not as dense) mixed with lead or bismuth salts from the styphanate / oxide results in the primers that blow into the case. I have found it to be helpful to add a lot of salt to the cleaning solution (luckily I have a sal####er aquarium tank so I just use half water from that source). Metal salts and some tars dissolve much better in incredibly salty brine solutions (wikipedia: Uncommon-ion effect, page: Common-ion effect) compared to just pure water. Just remember to wash the brass cases VERY thoroughly afterwards.
If your sonocator is big enough (and deep enough), I would recommend placing a separate container of metal in it so that you are able to stand up every single case by placing the boltface flush to the very bottom of the container as opposed to just laying them horizontally all over the place. I have found the best results doing this and even so far as cleaning the primer pocket neatly if I deprime them prior to cleaning them (which I do by either using water pressure in a bucket or buy placing the lee decapp/resizer primer punch as low as it can be to only punch it and not resize it)