I assume you're measuring light rather than sound, using a photocell and amplifier circuit attached to a sound card input.
I think your graphs look right, but for the shot at 1/500 sec, f:3.5, I'd measure the peaks of the curve when the shutter is fully open. Of course the shutter is more efficient at small apertures than at large apertures, as ic-racer posts above.
The thing to do is test and be aware of the issues. For instance, if you're in low light shooting wide open and need a shutter speed around 1/15 sec, the efficiency of the shutter can make a difference, but if it's on the slow side, that might compensate for inefficiency.