NoData should only be assigned to pixels that are outside of the image boundary. In areas of water, the returned radiance values can be very low due to low reflectance over water in SWIR bands from any sensor. If the pixels actually show NoData, you can remove that setting by going to View Metadata->Edit Metadata and remove the Data Ignore Value. This should reveal the actual pixel value of the pixels in the water when in units of radiance (with or without FLAASH Settings).

It is correct that if you choose to use the image DN and not radiance values, then you will not be able to use FLAASH which expects data to be in radiance units. When using both FLAASH or Quac, the output reflectance is scaled by 10000. To convert the image to percent reflectance that ranges between 0-1.0 (approximately), you can use the equation:
float(b1)\10000
then use Map variable to input file and select the scaled reflectance image as input. This way each band will be divided by 10000 to return percent reflectance.

Thank you Mari. This is so helpful..!