I don't know exactly how high the waves were, but I liked the effect.
I started using the 'Big Waves' mod even before it was in SH3 Commander. AILantic said he experimented with wind speeds up to 45 m/s, but it always defaulted back to 15, so increasing the wave height was the only way to go. I used the 'Seasonal' setting for a while, but came to the conclusion that even when it was using x1 during summer the crew still acted like it was a full-blown storm, so I was back to the problem of them refusing to fire guns in what looked like a calm sea.