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I think I might just be over thinking this but..

Under the Recon Drones wargear on pg 38 it says the drone has a BC, Homing Beacon and a Positional Relay.

Then it has the Special Rule turret mounting.

Does the special rule "Turret Mounting" mean you can only use the Beacon and Relay when its embarked on the Devilfish or can they both be used while not embarked?

No, when embarked, the Vehicle counts as having the homing beacon and positional relay

Indeed, there is nothing in the Turret Mounting section stating these two pieces of war gear are limited to when the model is 'embarked' on the transport. As they are provided as part of the basic war-gear, the model has access to these independent of any transport that you may or may not embark them on. The rule is there so you have an easy way to access these pieces of war-gear even when the pathfinder team is in a transport.

Think of it this way:
Fire points grant the ability to shoot out of a vehicle, does this mean all units need to be embarked in transports before they can fire their weapons?

look at it this way; you have rules A, B, and C.
Rule A has a set effect.
Rule B has a set effect.
Rule C grants rules A and B to certain specific vehicles while the bearer or A, B, and C is embarked upon that vehicle.

You always have Rules A, B, and C; it is just that rule C also grants Rule A and B on the vehicle you are embarked upon