Joystick Selection

So from what you are saying one joystick is Ex rated and hence requires no intrinsic safety barrier (or intrinsic safety isolator) and the other is a standard joystick which is protected by an intrinsic safety barrier (or isolator).

Yes. Either would be fine for Zone 2 BUT for the standard joystick with intrinsic safety barrier (or isolator) option you need to ensure the intrinsic safety conditions are met and the correct barrier(s) (or isolator(s)) are specified. This shouldn't be a problem if it is a standard passive resistive element joystick (becomes more complicated if the joystick has active elements such as motorisation).

IS requires a bit more work to initially design but will likely be cheaper (even when taking the equipotential earthing into account when using zener barrier(s)). In the end both options are acceptable so you can use either (they are just different hazardous area protection techniques).

<...Can a potentiometeric joystick connected by an I.S. barrier be used in a Zone 2 area without any additional certification....>

Yes, provided all circuits are protected by certified Ex i barriers and the L/R ratios of the cables fall within Ex i parameters. Switches and potentiometers are "simple apparatus" under Ex i, as they are non-energy-storing devices.