1) Will it be a problem to get a PCC, given that a 498A is pending against me?
For renewal of Visa or Passport in the country where you reside now, the formalities required to be complied are to be duly complied. However, this being an offence related to matrimonial disputes and since the case is being properly represented as also there is no restriction by court to travel abroad, you may, if required, give an affidavit to this effect and an undertaking to attend he court in India on being summoned, this will help you get your visa renewed.
2) In case I go ahead with PCC and the PCC came negative will the High Commission of India in UK conpound my Passport?
They may not do so but may seek for your deportation from that country to India. As per law, you are not supposed to take up an employment outside the country when there is a criminal complaint pending against you, whether it is false or anything.