There is no uniformity just as there is no uniformity in issuing standards.
VA destroys prints and most cities no longer require them. It didn't matter for me because anyone in the military has already been printed. FBI maintains multiple databases. They have databases on convicted felons, databases on fugitives, databases on fingerprint evidence, and non-criminal databases. To my knowledge there is no way to "get out" of the database once you are added. I might be wrong though.
VA statute on fingerprinting & CCW.
As a condition for issuance of a concealed handgun permit, the applicant shall submit to fingerprinting if required by local ordinance in the county or city where the applicant resides and provide personal descriptive information to be forwarded with the fingerprints through the Central Criminal Records Exchange to the Federal Bureau of Investigation for the purpose of obtaining criminal history record information regarding the applicant, and obtaining fingerprint identification information from federal records pursuant to criminal investigations by state and local law-enforcement agencies. However, no local ordinance shall require an applicant to submit to fingerprinting if the applicant has an existing concealed handgun permit issued pursuant to this section and is applying for a new five-year permit pursuant to subsection I. Where feasible and practical, the local law-enforcement agency may transfer information electronically to the State Police instead of inked fingerprint cards. Upon completion of the criminal history records check, the State Police shall return the fingerprint cards to the submitting local agency or, in the case of scanned fingerprints, destroy the electronic record. The local agency shall then promptly notify the person that he has 21 days from the date of the notice to request return of the fingerprint cards, if any. All fingerprint cards not claimed by the applicant within 21 days of notification by the local agency shall be destroyed. All optically scanned fingerprints shall be destroyed upon completion of the criminal history records check without requiring that the applicant be notified. Fingerprints taken for the purposes described in this section shall not be copied, held or used for any other purposes.
Contrary to popular belief (I blame CSI) nobody does a fingerprint match of CCW fingerprint against FBI entire fingerprint database. Fingerprints (and photos) are only used as additional confirmation/validation for possible match. Say you and criminal Joe have same name, and bad luck for you same DOB. It can happen right. Your application gets sent to FBI criminal database and that generates a partial match. Police look at partial matches because criminals often change names, or get fake/new SS numbers, etc.
So you data generates a partial match. How does the state know if it is mistaken identity or if really are "criminal Joe" (pretty stupid Joe)? Simple the record is reviewed manually by an analyst at the FBI who looks at thing like the prints, the photos, and your description (all things indicated in criminal records). Based on that they either confirm or deny the match. Some but not all fingerprints have been electronically indexed by gross classification. This isn't enough for an exact match but it can provide a negative confirmation. Kinda like blood type. If the blood at scene is O and you are O that isn't proof it was you on the other hand if you are AB then it is proof that blood isn't yours.
However nobody "runs the prints" = try to match your prints against FBI databases of criminals or unsolved crimes. That simply requires way too much time, money, resources for a resource that is very valuable and routinely backlogged. Anybody who knows anything about databases knows a full scan is going to take a while especially on something that contains more than a hundred million records.