Short answer. Yes, but only if the pardon expressly says so. Article 40 provides that a commuted or pardoned death sentence still carries perpetual absolute disqualification and thirty years of civil interdiction, unless those accessory penalties are expressly remitted in the pardon. Note, though, that Republic Act No. 9346 now prohibits imposing the death penalty at all.
What the law says
shall carry with it that of perpetual absolute disqualification and that of civil interdiction during thirty years following the date of sentence
Revised Penal Code, Article 40 — Death: Its Accessory Penalties. Read the full provision →
What the law says
unless such accessory penalties have been expressly remitted in the pardon.
Revised Penal Code, Article 40 — Death: Its Accessory Penalties. Read the full provision →
The default: accessory penalties survive commutation or pardon
Article 40 addresses exactly the situation in your question: a death penalty that is not actually carried out because it was commuted or pardoned. The article states that such a sentence shall carry with it that of perpetual absolute disqualification and that of civil interdiction during thirty years following the date of sentence. So the default rule is that these two accessory penalties stay attached to the sentence even after the death penalty itself is commuted or pardoned — commutation or pardon of the principal penalty does not, by itself, wipe out the accessory ones.
The express-remission escape valve
The article then gives a specific way around that default: the accessory penalties fall away unless such accessory penalties have been expressly remitted in the pardon. The key word is 'expressly' — the pardon has to specifically address and remit the disqualification and civil interdiction, rather than the accessory penalties disappearing automatically just because the underlying death sentence was commuted or pardoned in general terms.
What perpetual absolute disqualification and civil interdiction mean
Under the article, perpetual absolute disqualification and civil interdiction for thirty years are the two accessory penalties in question. These are consequences that attach on top of the principal sentence itself, restricting rights separately from whatever happens to the death sentence through commutation or pardon. Article 40 treats them as running with the original sentence by default, which is why an express remission is needed to remove them rather than assuming a general pardon covers everything automatically.
Why this article no longer applies to new sentences
It is worth being clear about current law here: Republic Act No. 9346, enacted in 2006, prohibits the imposition of the death penalty in the Philippines altogether. Where the Revised Penal Code's own terminology would call for death, the law now imposes reclusión perpetua, or life imprisonment where that terminology does not apply. So the scenario Article 40 describes — an actual death sentence being commuted or pardoned — is not one that arises under new sentences handed down today.