Short answer: No. If a court destroys the criminal file due to age, the defendant's criminal record lives on in law enforcement databases, be it local, state, or federal. In San Diego, the Superior Court records are open to inspection. Court case files are public records and subject to public inspection. California Rules of Court, rule 2.400(a) states that all papers in the court files may be inspected by the public in the office of the clerk. Rule 2.550(a) says that unless confidential or sealed by law, all court records are presumed open.
However, again, this does not impact a criminal history report retained by law enforcement. To get the conviction literally removed from the criminal history report, the defendant will typically need a court order directing the law enforcement agency to remove the arrest and/or conviction.
For example, in California, if the defendant can prove there was no reason to have arrested the defendant in the first place.
Specifically, Penal Code section 851.8 (b) requires “any law enforcement agency” to destroy their records. “[Penal Code] section 851.8 is for the benefit of those defendants who have not committed a crime. It permits those petitioners who can show that the state should never have subjected them to the compulsion of the criminal law -- because no objective factors justified official action -- to purge the official records of any reference to such action. . . ...” (People v. Matthews (1992) 7 Cal.App.4th 1052, 1056.) (Emphasis added)
In People v. Scott M. (1985) 167 Cal. App. 3d 688, 700 [“Section 851.8 is for the benefit of those defendants who have not committed a crime.”].) Factual innocence may be determined based on circumstances at the time of arrest or any meritorious defense. Recent case law establishes the pivotal time for viewing the evidence is when the motion is heard. The statutory language “necessarily means that the existence of reasonable cause depends on the current evidence rather than simply the evidence that existed at the time that the arrest and prosecution occurred.” (People v. Laiwala, 143 Cal. App. 4th 1065, 1068 & n. 3 (2003) (emphasis added).
Keep in mind in California, "expunge" does not mean to seal or destroy, but officially dismisses the conviction - leaving the public record intact.
The best place to start is contacting your local public defender and ask about post conviction relief or record sealing if your arrest did not result in a conviction. Getting free advice never hurts.