Change in the inventory

if goods withdrawn by owner of business, are not recorded in the books of account, does it hamper the valuation of inventory?

Yes, it makes inventory valuation incorrect. It is always incorrect from an accounting standpoint. In some jurisdictions, such an unreported taking would be illegal. Depending on local law, such takings may also be taxable under consumption or VAT schemes. And depending on your form of organization, they may be reportable as sales income by the business or compensation by the owner.