Hey there,
I'm trying to get my dad's 2011 E550 running after a few years of non use.

-I have access to inside the vehicle via key fob and manual key.
-Battery is completely dead.
-Cannot access engine bay because hood latch is broken.
-Cannot open trunk for battery replacement; our model does not have place for physical key at trunk.

Is there anyway to get the trunk open so i can access the battery? I saw some videos to tackle this but couldn't find one for our car model.

I also have one of those noco battery booster.

 

Try removing the license plate light socket to access the wires. Determine the neg. and pos. Connect a battery charger and see if that pushes enough power into the system to unlock something. Trunk a door try them all.

 

Remove front underside fascia panels to access hood latched from below the bumper is what I recall reading

 

Try to find the emergency latch from inside the trunk. Access from the pass-through in the rear seat.

Are you sure there is no hidden key for the trunk? Under the license plate flare on the E63.

 

Couldn't find info. with regards to key lock in trunk for your specific model, but did find that W211 and W219s have lock by rear license plate light (Just as our W212... as pictured above).