Using clone can be risky very risky if you don't check the implementation of this clone method... as you can suppose a clone impl can act in different ways... shallow or deep clone... and some developpers may not always check what kind of clone they will retrieve...
In a big application, big team, it's also risky because when cloning is used, if you modify the clone implementation you may modify the application behaviour and create new bugs... and have to check everywhere the clone was called (but it can be the same for other object methods like equals, toString...
When modifying the clone of a small subclass A (from Deep to Shallow clone for exemple), if an instance of B has a reference to A and a deep clone impl, then since the objects referenced in A are not shallow cloned, the B clone won't be a deep clone anymore (and it's the same for any class referencing a B instance...).
It's not easy to deal with the deepness of your clone methods.
Also when you have an interface (extending Clonable) and many (many!) implementations, sometimes you will check some impl and see that clones are deep, and call a clone on the inteface but you can't be sure at runtime all impl really have deep clone and can introduce bugs...
Think it could be better to impl for each method a shallowClone and a deepClone method, and on very specific needs implement customised methods (for exemple you want a clone and limit the depth of this clone to 2, make a custom impl for that in all classes concerned).
Don't think it's a big matter to use a clone method on a JDK class since it's not going to be changed by another developper, or at least not often. But you'd better not call clone on JDK classes if you don't know the class implementation at compile time. I mean calling the clone on an ArrayList is not a matter but calling it on a Collection could be dangerous since another Collection implementation could be introduced by another developper (he can even extends a Collection impl) and nothing tells you that the clone of this impl will work like you expect it to do...