I think what matters most is the substrate for the sweet flag roots.
If planted in very heavy compacted clay, then when the pond stays low enough for the clay to bake dry, your sweet flag will perish.
If planted in an uncompacted mixture of sand, silt, and clay, then I believe the roots will grow down the 18-24" to reach the available water in your saturated substrate.
I would be more worried about the plants being "drowned" for an extended period. During a big rain event, how long does it take your pond to go back to the full pool elevation?
