At first their attempts were pretty elaborate. They lifted a fingerprint from a glass a person had held and then used an acidic solution to etch that pattern onto a mold. This mold then opened all of the high-end thumbprint readers they had.
However, if I remember correctly, they then went low-tech and simply used a photocopy of the thumbprint which also opened several devices.
Of course that says nothing about other ways to defeat the cuffs, which would probably become the prime area of research at that point. (why attack the locking mechanism if there are easier to defeat weaknesses).
Handcuffs are designed so that one officer can put them on and another can take them off. If that weren't the case this situation of being able to print 1 key for all handcuffs wouldn't exist - they would simply make unique keys per handcuff.
However, in a broader view, yeah, there are probably better ways than fingerprints handle keys once electronic locking mechanisms are introduced. Probably something akin to a 2-factor cryptographic mechanism.
I feel though that my larger point is getting lost in this thread. It was/is:
Just because a security technology doesn't work for reason $x in situation $y, that doesn't mean that the weaknesses also apply to situation $z.
Two-Factor authentication (something you have + something you know) is for physical security as well as online.