The transmission upper mount is different, and would need the accompanying trans bracket for interchangeability between the DC and EK chassis.
The rear mount is different as well, as it is bolted on to the EK sub frame, which sits closer to the engine, thus needing a different smaller rear T-Bracket.
All the main mounts are different.
When I swapped out my 97 hatch sub frame and steering rack for a complete DC2 set up, I noticed how much longer the rear T-Bracket was. Made me wonder about the how the shorter T-Bracket (EK set up) would have less torque (stress and flex) transferred to the mount than the longer DC2 set up. Thus putting more torque where you want it. Maby they were able to get away with a fluid filled mount, with out tearing, due to the shorter rear mount set up.
But I hear ya, I just finished stuffing a B18C engine in my EJ6- and it does not have the same feed back as the DC2 chassis.
I'm guessing the EK9's motor mounts have the same part numbers as a 2000 Civic Si.?
I've found installing just the two front/lower torque mount inserts from Energy Suspension is enough to do the trick with out being over the top. They're inexpensive and easy to take in and out.