Does this practice contravene any state statute(s) or rule(s) of
Generally not. States could adopt a statute that says otherwise, but I'm not aware of states that do. States often have regulations limiting police use of biometric data for general, non-probable cause based searches for criminal suspects.
For example, many states don't make fingerprints obtained for professional licensing background checks available for searched by law enforcement without a warrant and probable cause.
I suspect that states may start to do so with rape kit DNA, but it hasn't previously been identified as an issue, so there aren't statutes that prohibit this in most cases (e.g. victim's rights bills have not thought to address the issue).
The reason for concern that could lead to future statutes is two fold.
First, including rape kit DNA in searches discourages people from reporting crimes because it might put them at a disadvantage in an unrelated criminal proceeding.
Second, the risk of false positives is vastly higher in a random search of biometric data from people with no articulated connection to the crime than it is when isolated individual suspects who there is probable cause to believe committed a crime are investigated. The chance of a false positive for someone in a database with millions of people is non-negligible even if the risk of a false positive in any one isolated comparison is tiny. Even a 1 in 10,000,000 chance of a false positive in a database of 40 million people will routinely produce false positives in random searches. And, while DNA evidence is very accurate, partial forensic DNA samples aren't absolutely incapable of producing false matches to nearly the same extent as a comparison of two complete whole genome samples.
So, states may adopt such statutes in the future now that the issue is in the spotlight.
contravene any federal statute(s) or rule(s) of evidence?
violate any state constitutions or the US constitution?
No. At least under current jurisprudence. The relevant provisions are vague legal standards that are applied with great discretion by courts. Evolving understandings of the situation could change that view in the future.
Footnote: Does doctor-patient privilege or HIPPA control?
There is a doctor-patient privilege recognized in every U.S. state and in the federal courts.
Forensic DNA obtained from a rape kit from a potential suspect isn't protected by the privilege since the suspect isn't a patient of the medical provider in that medical procedure.
There is an arguable case that the rape victim is a patient of the medical provider who gathers the DNA, including the rape victim's DNA for the rape kit, and that the patient has not waived the doctor-patient privilege merely by permitting the medical professional to use the rape victim's DNA profile to distinguish between sample material in the rape kit that is her own from material from a suspect. Moreover, such a waiver of doctor-patient privilege would probably not be legally valid unless the rape victim provided informed consent to that release.
The rape victim might also have federal HIPPA protections for the privacy of her DNA profile collected as part of her medical records under a similar theory.
Mostly, this hinges on how the relationship of the rape victim to the person administering the rape kit is characterized, and in particular, if gathering evidence in a rape kit is "medical treatment" that is privileged.
To the best of my knowledge, there is no case law interpreting either the doctor-patient privilege or HIPPA in a rape kit DNA fact pattern.
If it is considered to be a doctor-patient relationship for medical treatment within the meaning of the evidentiary privilege and HIPPA, and the DNA was shared on a database which law enforcement has access to without a warrant without the victim's informed consent, this evidence and all "fruit of the poisonous tree" derived from it, could probably be suppressed in a criminal proceeding against the rape victim, even if the evidence conclusively linked the rape victim to the crime.
Under the circumstances, and given the policy considerations and the lack of other controlling law, this would be an attractive interpretation of the existing law for a court to adopt.
If evidence completely independent of the blind database match provided probable cause that the rape victim committed a crime, and the crime was one in which there was forensic DNA evidence, law enforcement could probably get a search warrant to take a legally untainted DNA sample from the rape victim to compare to the forensically collected DNA evidence, however, just as it could with any other suspect.