1. No. Mere filing of 498A case against you will not deter you in getting PCC,
2. For the fact that 498A complaint has been lodged by your wife, your PCC will not be negative. However, hypothetically if it is considered that there is a negative PCC submitted against you, then also your Passport will not be impounded. Only extension of VISA, for which PCC is sought for, may be refused,
3. Relax.