>Was it unsafe to assume that she didn’t have any milk as I couldn’t see any when I gently pinched her teats numerous times?
That was the wrong assumption. Firstly, it is notoriously difficult to express a bitch - that is why you don't hear of breeders (often) using breast pumps or expressing milk from bitches for puppies. If puppies can't nurse, then formula is used. You are unlikely to get milk out of a bitch unless she is literally overflowing with it and it's bursting out of her - which isn't going to happen in the first 24-48 hours after birth.
As MamaBas says, sucking and nipple stimulation (in an ongoing way) is what causes milk to come down.
>If yes, is it too late to stop supplementation and let them nurse fully?
Of course you should be keeping puppies and mum together as much as possible and allowing mum to act naturally and feed them. It's not just about feeding them, it's about licking them, nurturing them, cleaning them, mothering them generally. Research shows that puppies whose mothers have licked them and cleaned them a lot and been 'good' mothers grow up to have better stress responses and immune systems than puppies with 'bad' or neglectful mothers. Mothering is not just about feeding.