Settle itself is rarely affected by floodwater, although surrounding villages/roads may be under water for a short time after vey heavy prolonged rainfall. There are a number of decent tracks so it needn't be a continuous bogfest if you pick the right route/walk. The waterfalls around Settle are well worth a visit when in full flow, so bear that in mind.
Don't hear anything about Malham being a flood risk, although the PW path, heading south, can be under water a short distance outside of Malham and the path itself can be boggy. Main path to the Cove will be passable and the only danger is wet and slippy limestone. Similarly with Gordale Scar/Janets Fosse - and if the path is difficult then there is the alternative of taking a road walk to the Scar or Fosse.