I try very hard to not let them get below 50%. You just never know when you might have to stay down a long time. I can run 5 hours at 3kts and my batteries are at about 75%. When I surface, they will fully recharge in around 55 minutes. I usually run at 50M submerged. That is usually deep enough to keep from being spotted from the air. If you run too shallow, your sub can be seen from the air through the water.
BTW: The 3kts is barely 3kts. When I select it, the printing readout and voice will say 2kts but, under the speed dial it will read 3kts.