I concur with Prerana for not to pay interest on overdrawn capital. Logic being - a business & its owner are separate entities as per company's act. Hence at all times, the business need to look at its capacity to pay to preferential creditors or stakeholders. In the given case, the business is not earning or doing well; in such case owner/ proprietor/ shareholder should not lay claim or be paid interest on his capital.
And now assuming, interest is paid - I disagree with Aditya. Income tax act does not distinguish a business with eroded capital or otherwise. It requires the entity in question to deduct TDS at all times if it falls within the ambit e.g. not a bank or such institution as notified.