Your spouse had not deposited her income in previous years in bank. But had she accounted for those income not deposited, in her returns for the respective previous years? If so she need not pay income tax again on those amounts. There is a law against exchange of large amounts as cash between individuals. But there is no legal limit to the amount one can deposit as cash in a bank account. Under which head your spouse is showing her income in the tax returns? If she is showing her income under the head “Other Sources”, there is no need to maintain accounts. But if she is showing under the head “Profits and gains from Business or Profession” and the gross income is above a certain amount, she will be required to maintain books of accounts. The reason is that she will be entitled to deduction of certain expenditures to compute her taxable income. Normally one does not submit bank pass-books along with the returns. The bank doesn’t suo moto send your accounts to your Income Tax Officer either. In the very unlikely event of the Income-Tax Officer asking for the passbook, you explain as you have written above. Do not worry. Both of you have good peaceful sleep.
If the Income-Tax Officer gives you problems, contact me. I shall tell you what to do.