The most obvious sign is the air box. The DNE engines have their airbox on top (mukhang carb air filter) while the DE engines have their airbox after the tube, behind the battery.
The DNE engine is supposedly tuned to take lower fuel quality i think. It has around 5hp less on paper then the DE (105hp vs. 110hp).
Why some people complain the GA16 is a bit weak (esp on the heavier B14 body): when dynoed the GA16DE is found to be quite poor on the wheel HP ratings but when the basic bolt-on mods are added, it is very responsive. To share a bit, some guys get around 80hp at the wheels more or less when they were dynoed with the stock set-up. They added a free-flow filter and headers, then did some fine tuning and it would give a very healthy 100hp at the wheels (this was with the B13 of my friend). SCC also did a project GA16 beofre with some bolt ons (JWT ECU, JWT cams, intake and exhaust) and it gave the engine the around the same wheel HP as a Honda B16, with more torque.

What was found is the stock parts (intake and exhaust amongst some) are quite restrictive but when changed, you have avery good engine to work with.