Storms happened.
Subs at times were unable to sink ships due to storms or pea soup fog.
The hydrophone/sonar method worked only a skant few times, and often it was just sheer luck.
Be warned, you may not be able to see the other ship, but some of them (the ones with guns) can and will see you before you see them in most instances, and somehow gain pinpoint accuracy and plant a shall right onto your deck. This is a bug, but it is there.
I leave the fog attacks to the arcade gamers out there