Hibernate's org.hibernate.query.CommonQueryContract has setTimeout() method, examplified as below:

var query = ... // create some query (selection/mutation HQL query, Criteria and native query)
query.setTimeout(int timeout);

Internally the above method will end up with invoking JDBC java.sql.Statement's setQueryTimeout() method, which we could implement by invoking Mongo Java driver accordingly.
 
This is a generic feature applicable to all kinds of Hibernate Query, including selection/mutation HQL query, Criteria, and native queries.
 
Addressing the source code notes tagged with TODO-HIBERNATE-55 is in scope of this ticket.