Jeff,
We should compare notes more often. I, too, had the mysterious thumping noise that you describe and had no idea what it was. But, I also had the flashing gas gauge and P0455 fault code (gross leak, evaporative emissions system). I found a similarly disconnected hose, but it was in the center of the wiring harness tray where the hoses from the two purge valves meet with the main hose going back to the charcoal canister. I'm surprised you didn't have the fault indications.
http://www.benzworld.org/forums/w140-s-class/1346673-p0455-code-problem-solved-i-think.html
I never read your post because it was titled EGR valve. To my knowledge, the V12 doesn't have an EGR valve (at least the OBDII 1996 and later models). I've never seen it mentioned anywhere in alldatadiy.com nor have I seen anything that might be an egr valve in the engine compartment. The only thing attached to the exhaust side of the cylinder head is the air injection valve.
At any rate, I reconnected the evap system hosing, and the fault code has stayed away, and now that I read your post, I realize that the thumping sound is gone. I never connected the two issues before now.
Brett