When performing squats when you come up should u lock your legs (straight legs locked knees) so they are as straight as they can go or should you stop just short of full lock then continue with next rep?

To be honest, its not a huge issue (and it wont affect your quad balance if this is where you are coming from). The thing about squats is that it is not really a quad-centric exercise. What IS important is strong posterior chain engagement, and locking out the hips at the top.
Most involved with heavy squat do lock out everything at the top, then take a breath, drop, then exhale on the way back up.
This is a good tempo guide, increases rep by rep focus, and also, lungs full of air on the way down helps stabilise the movement in some ways.

You are not a bodybuilder- stop obsessing about your quads, its all about posterior chain and your core now

I just wanted to make sure, because the personal trainer guy i had told me not to lock, then i wondered if by locking for these past few years it had contributed to my bad knees!!

nah, I lock out when I squat. Just a handy way to take a breath before doing the next rep. Most important thing in a squat as far as I am concerned is good posture with the back.