Poa in filing section 138 nia cases

yes he can.

Inthat case who should sign on the Vakalatnama? The original victim or the POA Holder

If complaint is filed  through power of attorney holder than definitely power of attorney holder wil sign the vakalatnama.

No clear cut authority available on this. Ideally only the individual named on the cheque must file the complaint and he must give evidence, but following proposition also emerges out..

If POA is executed just before filing the complaint and for the case purpose only, in that case

1. Complaint can be filed by the POA Holder, he can give evidence only about this GPA/SPA.

2. POA holder cannot be examined in place of original payee, so cognizance can only be taken after examination of payee individual.

if POA is executed (as GPA) much prior to case and authorizing the agent, to act on behlaf of the individual for the said transaction, then.

1. A fresh SPA can be issued in the name of this agent, not only to pursue the complaint but then he can be examined under S.200 on behalf of payee individual also.

The catch is that an existing GPA holder (at the time of transaction) can be authorized both as complainant as well as competent witness on behalf of original payee. 

This is still the grey area, even recent Supreme Court order in A.C. Narayanan vs State Of Maharashtra & Anr. on 13 September, 2013, has left some questions open on this issue.