What would have been future perfect in direct speech becomes pluperfect subjunctive in past indirect speech.
The direct speech would have been:
"Hostium," inquit, "numero habebo, si aut Ambiorigem aut eius legatos finibus vestris receperitis."
He said: "I will consider you as enemies if you receive (lit. will have received) either Ambiorix or his ambassadors into your territory."
The past indirect speech becomes what you've quoted, meaning "He affirmed that he would consider them as enemies if they received (lit. had received) either Ambiorix..."
This literal "had received" doesn't mean an action that had been completed before the time of speaking but an action that would potentially be completed before that of considering them as enemies.
For more on the sequence of tenses and such in indirect statement, you can read Dantius's post
here.