No, you won't be penalized for failure to take a distribution (RMD) if there isn't anything to distribute.
To prove that, however, the IRA custodian needs to report the FMV of the account ($ 0?) on Form 5498; this is the same form that reports the RMD amount.
The information on Form 5498 is submitted to the IRS by the trustee or issuer of your individual retirement arrangement (IRA) to report contributions, including any catch-up contributions, required minimum distributions (RMDs), and the fair market value (FMV) of the account.
See Form 5498 IRA Contribution Information
