The SMS's automatic software most likely leaves the EQ's at their default frequencies (that would massively simplify the number of variables being addressed), so if a null hit at one of those EQ frequencies it would probably increase the EQ to the max. The danger that exists with manual EQ is that you can stack two EQ channels at the same point and push both to the limit to address such a null - at which point the sub's driver is being asked to operate at 12dB higher output at that point than the baseline, which could be considered similar to asking the sub to run 12dB "hot" (something that could be painful to a driver when you throw some deep bass at it).