I think the main issue here is that when you're developing a type system, you generally want the types to classify objects into certain categories that tell you things about them. So if I define some kind of a reference type, what I am saying is that an object of that type is a kind of a pointer to something.
So now, if I allow null references, then my reference type is really saying that "objects of this type are pointers to either something or nothing". That's all well and fine, but it makes the type less precise, in that it conveys less information about the object it is categorizing.
As it turns out, this lack of information is quite important because one of the most common things you have to check when you're given a possibly-null reference is whether or not it is null. You need to insert "if (ptr == NULL)" all over the place. Thus reference types which allow null references ultimately give me less expressive power.
Most of the time null references are created because either an error condition must be reported (e.g. malloc fails), or it is unclear at some point in time whether or not an object exists. Error conditions can be better signalled using exception handling. As for cases where you're not sure if the object exists or not, then one possibility is to use an option type like in Standard ML:
datatype 'a option = SOME of 'a | NONE
This is a polymorphic type that says that either the object exists or it doesn't, and you can find out what the situation is by using a "case" statement on the datatype constructors:
case foo of
| NONE ==>
Thus by combining a reference type without nulls with an option type, you can create "reference option" types, which have all the flexibility of "with-null" reference types.
But the cool thing is, you only ever need to check the "null-ness" of the object only once; once you do the check, you're handed a reference object which is guaranteed to be non-null. Thus you can easily partition your code into parts that will do the non-null check and those that assume all references handed to it are valid.
This is why a good type system can make programming so much cleaner and easier