Quoting from Hibernate documentation, 14.4 Forms of join syntax:
"The implicit form does not use the join keyword. Instead, the associations are "dereferenced" using dot-notation. implicit joins can appear in any of the HQL clauses. implicit join result in inner joins in the resulting SQL statement. "

However, when I use something like this:
SELECT COUNT DISTINCT A.id from A where A.B.C.id=1;
in generates
select count(distinct a.id) from tbl_a a cross join tbl_b b where a.b_id=b.id and b.c_id=1;

Mapping:
<class name="A" table="tbl_A" >
<id name="id">
<generator class="native"/>
</id>

<many-to-one name="B" column="b_id"/>
</class>

<class name="B" table="tbl_B" >
<id name="id">
<generator class="native"/>
</id>

<many-to-one name="C" column="c_id"/>
</class>

Can I convince Hibernate to generate a "inner join" instead of a "cross join" and still using implicit join?

Have you resolved your issue?