Is that using the mod that adds the option to turn them on and off from the hotbar? You might want to contact the mod author in that case.
Otherwise I'm pretty sure you can still turn them on and off if you link an activation module to the Bobby AI, and use a wireless controller linked pair you control from another activation block on the main ship, linked to a inner ship remote so you can turn it all on and off from the hotbar.
The mod does save space and effort though, if you get it to work.
First things frist:
if you put the turret rail on your hotbar it's not for turning on or off turrets, but for actually controlling the aim and shooting.
There is a option in Bobby AI to actually aim manually with them.
If you want to turn on or off your turrets, you should install a mod from the ingame mod list (accessable in main menu) called "Turret Hotkey".
You'll get a little marker on the left side of your hotbar, showing you if turrets are on or off. you can turn them on by pressing 'J' and turn them of by 'L'