First, what is a clearance certificate?
If you are acting as the executor of an estate, you will be required to file a tax return for the year of death. Once you have that back from CRA, you can apply for a clearance certificate, which gives CRA a final chance to audit the deceased person.
Generally, you will want to apply for a clearance certificate, because it gives you peace of mind that there are no further taxes owing. This is especially true if you are the executor but not the sole beneficiary, but even if you are the sole beneficiary, it can be helpful to know that CRA is not coming back to you while the estate money is still separated from your own. Ultimately, this is a discussion to have with your lawyer and accountant.
For a great post on this, check out this.