Hi Sandra,
The following query will give you all methods and constructors annotated with @Deprecated:
from Callable c
where c.getAnAnnotation().getType().hasName("Deprecated")
select c.getDeclaringType(), c
It won't give you, however, elements whose Javadoc contains a tag @deprecated. We are preparing a version of SemmleCode that populates Javadoc, which will allow to spot those too. Thanks for bearing with us.