Rainbow trout population estimates N are calculated using the Modified Petersen equation
N =[((M+1)*(C+1)) / (R+1)] – 1
Where M is the number of fish marked, C is the number of fish captured and R is the number of fish recaptured.
I didn't write it. I distilled it it from this report - http://www.southforkboise.org/wp-content/uploads/2011/07/Hebdon2006SFBdraft.pdf
The number of fish surveyed from a float boat is a very small percentage of the total. The numbers encountered using a more intensive survey technique like a canoe as part of the electro charge and a large number of people netting is higher, but you cover less water.
As a volunteer netter on one of the wading crews the fish were not in the large bucket very long. A few minutes and once the can was getting full we would pull over, count and measure. Usually someone would freshen the water. Mainly there was a focus on quickly getting the fish counted, measured and put in smaller buckets with fresh water and then walked upstream about 100 yards or so for release (that was my job). I do recall some mortality to whitefish. They seemed to be more vulnerable. Once I remember one large brown trout looked really bad and the crew worked on it and revived it. Bottom line is the IDFG crews I worked with showed concern with impacts to the fish being sampled and they pay attention to their methods. That's my take on it as a layman. But I am sure you can get good insight from Greg Schoby.