I think this limitation is only possible when the SHIELD hatch itself has large parasitic capacitance(CP), for example big size washing machine touch panel with water proof feature. The characteristic of this kind of boards is big size board plus large shield hatch area(large shield cp), the sense clock divider calculated by SmartSense may not satisfy the shield hatch be fully charged and discharged during sensor scanning (waveform on sensor and shield are not synchronized). This may cause poor SNR or sensors.
For small size touch board, use shield and SmartSense together is not a problem. For Manual with Run-Time Tuning or Manual mode, you can set the sense clock divider by yourself, so use shield and SmartSense together is also not a problem.