---%<---
$ rm *.class; cat A.java B.java C.java; javac C.java; javac -version -Xlint:deprecation C.java
@Deprecated
public class A {}
@Deprecated
public class B {}
public class C {
    @SuppressWarnings("deprecation")
    A a;
    @SuppressWarnings("deprecation")
    void m() {
        B b = null;
    }
}
javac 1.5.0_08
C.java:3: warning: [deprecation] A in unnamed package has been deprecated
    A a;
    ^
1 warning
---%<---

It seems that @SuppressWarnings("deprecation") works fine for local variables but has no effect on fields whose type is deprecated. Adding @SuppressWarnings("deprecation") to the class does not help either.

Same bug in JDK 6 b95.
Another more comprhensive test case:

@Deprecated
class A {}
class B {
    @SuppressWarnings("deprecation")
    A a;
    
    @SuppressWarnings("deprecation")
    A m(A a) {return null;}

    @SuppressWarnings("deprecation")
    class C extends A {}
}

Which gives the following warnings:

TestX.java:6: warning: [deprecation] A in unnamed package has been deprecated
    A a;
    ^
TestX.java:9: warning: [deprecation] A in unnamed package has been deprecated
A m(A a) {return null;}
^
TestX.java:9: warning: [deprecation] A in unnamed package has been deprecated
A m(A a) {return null;}
^
TestX.java:12: warning: [deprecation] A in unnamed package has been deprecated
class C extends A {}
^
4 warnings