First of all...I have moved your thread to the appropriate area and welcome to SubSim
When a ship sights you or is attcked by you it will start zig zagging but will maintain a mean course. The exception being if it nears a pre-set waypoint there is a possibility said instructions will be fubar'd and a 'scattering' effect will be the result.
Commander will give you the option of variable reload times for the deck gun and the ability to adjust wave height from standard to 1.25x, 1.5x, 2.0x and seasonal which will have an effect on the pitch and roll of a ship as well as your boat.
GWX only allows you to use HE shells but it is possible to put the AP shells back into the game.
There are mods out their IIRC that have tried to change some of the above with varying degrees of success over the years since the release of GWX...heck even I've made a mod that allows a larger than the norm amount of shells to be carried by your boat as well as one that allows said deck gun to be used in ALL weather conditions.
Give GWX a go, you may be surprised, it is certainly better in all departments than stock/vanilla SH3.