If she isn't displaying the behaviour because she is getting rewarded for it i.e. you coming to see her, and then you squirt her with water all this will do is associate seeing you with a bad thing - water in the face from time to time.

If she stops because you go donw then you need to stop going down to see her as having you there is her reward for barking and teaches her that if she barks she gets attention. Like you say Collies are extremely smart but any dog will pick up on this.

Seeing you should be a positive experience (it is now and that is why she stops barking) but when she runs the risk of getting a face full of water every so often she is going to lose this and you will only distance the dog for yourself.