In case of proprietorship firm there cannot be two natural accused (more than 1), simply because S.141 is not applicable on proprietorship firm.
Now the point is the mandate holder, can be an employee, or a relative, or even two joint signatories with authority from proprietor, these people cannot be made accused as per reasons above and also account is of proprietor not of these people.
Coming to the second question, in CPC, there is a provision, that if plaintiff makes mistake (or ignorant) about constitution of the respondent firm, then it is on respondent to come forward and state the exact nature. But in criminal under S.138 the offense is not when cheque dishonors, but it is when notice is given and no payment made. So I am sure complainant will not be able to prove that real proprietor indeed received the notice. If the prop firm is also made accused (which itself is non maintainable) then it can be argued by applicant in his favor. Yes, power with the court is there to add, but since NI Act is special act, you never know how the court would decide. One thing is sure mandate holder cannot be convicted, but prop can be added or not at this stage, doubtful.
Another aspect trial is at decision stage, you stated court was about to acquit, so is this sole ground for acquittal, if the case is getting decided in favor of drawer on merit, then should not be a problem.
