In general, but it depends on the person performing the lock, the person in the hold, and how much they know about each other. It also depends on the locks themselves, different techniques do different things and rely on different angles to create pressure. Joint locks are, in large part, about creating leverage and putting the joint on an angle where it becomes painful for it to move. So, it follows that it’s more difficult to put someone with greater flexibility in their joints in a lock because you have to bend it further than you’re used to.
You create leverage, apply pressure, and that causes pain because the joint bends in a way it’s not meant to. And, yes, if you’re not in pain then it’s easier to escape. More so if you’re opponent doesn’t know and isn’t used to working with a training partner who is double jointed, since they’ll initiate the technique to the point they’re used to then stop. This can give the person who is double jointed (or any person who is not fully in the lock) a means to escape, since they aren’t actually trapped.
In short, yes.