I think Goldenrivet is right about depth having no affect on hydrophon performance.
As far as how often to do a check. I figure so: if my cruising speed is 5.75 knots (in a type II), and the range of the hydrophon 20 kilometers (estimate), then submerging every two hours or so will prevent ships travelling at 6 knots (slow traffic) from sailing passed me just out of visual range (8 km). If your cruising speed or the speed of intended targets is higher, then you've got to submerge more often. If the range of your hydrophone is greater, less often.
Some people stay submerged as often as possible, and I like to wait submerged at key high-traffic areas.
I asked a similar question some time back:
www.subsim.com/radioroom/showthread.php?t=133456