How to express in datalog that the entity is referenced by some other entity (but I don't need to capture info about referencing entity)?
A reference is a fact like any other. You can check if the fact is present.
[?person :person/children _]
Matches if ?person has a fact with attribute :person/children. Meaning ?person has a reference to a child.
(You can elide trailing _, so you can write [?person :person/children])
Other way round:
[_ :person/children ?child]
Matches if ?child is referenced by some entity through the :person/children attribute.