Are there any plans to issue an update to the Signal Scope app to account for this change in the hardware?
In short, no. The lowest frequency signals are essentially driven into the noise floor by the iPhone's high pass filter. "Compensating" in software cannot bring back signals that are already lost, and it won't improve the SNR for those frequencies which have not been totally lost.
It's unfortunate that Apple decided to apply such a filter in the iPhone 3GS (and a less destructive one in the iPhone 3G). Ironically, for flat headset mic input response, the original iPhone is the best option (see the blog