Ah, the Mantu.
Let me start off with the disclaimer - short answer: no, the Mantu are not the Nephilim.
The longer answer is that the two are actually quite distinct.
The Mantu are a 'historic' enemy; they fought two conflicts with the Kilrathi - a war which ended in a draw in 2431 and then a brief skirmish in 2598. Per Prophecy's ICIS manual, the Mantu are a race of insular explorers who were probably attacked by the Kilrathi in the first place. The Kilrathi spent two hundred years demonizing the Mantu as being an ultimate evil, just as they have begun to do with humans in the TPoF novelization (creating a cult around Blair's destruction of Sivar).
The Nephilim, however, are much more ancient: they are the 'Star Gods' which appeared around 1600 BC and challenged pre-historic Kilrathi to a conflict. Finding the Kilrathi "unworthy" of trial by combat, the Nephilim ordered them to advance themselves through conquest. The Nephilim promised to return either to conduct the ultimate test or to wipe out the remaining Kilrathi should they ever fail in battle against another species. This formed the basis of Kilrathi religious belief, and is one of the reasons for their expansionism (and, somewhat appropriately, their fear of losing in battle to the Mantu and the humans).
Read on for some discussion of the history of the subject.
The assumption is usually that Origin asked Dr. Forstchen to include the Mantu in the novels as a reference to future events. Rather, the exact opposite is true - the author took the initiative and created the references based on then-vauge possibilities for the future of the series.
The Mantu's inclusion in Fleet Action (and then the two game-based novelizations) was based on a conversation between Dr. Forstchen and David Ladyman about the long term future of the Wing Commander series. Origin had already decided to end the Kilrathi conflict in Wing Commander III, and the vauge plans for the future were that a new alien enemy would be brought for future games. Forstchen siezed on the possibility and began to reference the Mantu, a historic enemy whom even the Kilrathi feared.
Origin, of course, went with the 'human versus human' Wing Commander IV story and the vauge future aliens remained vauge. By the time development of Prophecy began, the Mantu had been developed somewhat (see above) in novel references... and the Prophecy team decided to create a new race with a distinct backstory (see above again). Prophecy's ICIS Manual includes a 'retcon' explanation of the Mantu, claiming some of the above to explain why they weren't actually a threat to humans.
Note that one novel published closer to Prophecy does contain a reference to the Nephilim: Action Stations' talk of a warlike empire coreward discovered by a Confederation deep space probe is in reference to the Nephilim rather than the Mantu.