What are the scientific consequences of the lost of the Nereus submersible?
Nereus as is, is currently not replaceable, but it was insured at a replacement value of $3.1 million, and my understanding Woods Hole currently plans to replace it, though unlikely at this point that there's a solid timeline for this taking place.

Landers, fish traps, and sediment core samplers will still be actively used, but again, these are not really comparable to the areas of research that Nereus was able to cover. 

UPDATE: These appears to be the last log entry for the Kermadec Trench 2014 expedition, and the official statement on the day of the event.