Actually the catenary has nothing to do with the Acela's not having an upper level. Amtrak's Capitol Limited operates under the catenary for a short distance to reach Washington Union Station. Additionally VRE operates double decker cars into Washington, as does MARC and they also clear the catenary. Moving north the LIRR operates double decker cars through the East River tunnels into Penn station, under catenary. And coming soon, New Jersey Transit will be running double decker cars from Trenton to NY underneath catenary.

The limiting factor has always been the tunnels on the NEC, which won't clear a normal sized double decker car. Most of the commuter RR's mentioned have engineered a reduced height double decker car, that clears those tunnels. Amtrak however overall, has decided that those reduced height cars make storing luggage very difficult. One can barely put a thin briefcase on the overhead luggage racks, much less a suitcase.

Since most passengers riding Amtrak tend to have luggage, Amtrak has stuck to single level equipment for the NEC.