Like many other things, getting the crew to man the deck gun is troublesome, intermittent, if not downright broken in the current version of the game...hopefully Patch 1.2 is going to fix it.
Here's a few workarounds that might help...
You can climb down the outside ladder from the conning tower onto the deck and go and man the deck gun yourself which also brings the gun crew to the station..... however, this really isn't always very practical for a Captain with other tactical/navigational considerations.
It's been a few weeks since I've been out on a patrol, but from memory I'd usually just view my target in UZO or binocular view...
press spacebar while viewing the target to select, and the gun crew will man the deck gun and start firing.
I've just installed TheDarkWraith's New UIs Mod which includes the old style officer icons on the HUD, allowing direct orders (basically the same as SH3). With this you can order the Watch officer to have the deck gun manned and they will actually do it..... hahaha... no need to reach for the Walther....hahaha
Hope that helps, mate.