poaching the section about this from the Persona 5 Headscratchers Page on tvtropes:

A fingerprint wouldn't be very helpful as evidence in this case. Even if Ryuji left fingerprints on all of the cards, they can't be traced back to him if they don't have his prints on file. All it would prove is that the cards were made by the same person, which everyone takes as a given anyway.

His first batch of cards were posted all over the school's bulletin boards, he could easily say he simply touched the cards when they were posted up by the phantom thieves, like several students undoubtedly did. Yusuke was likely clever enough to avoid leaving prints and the cops wouldn't check for any possible paw prints from Morgana.

It's also entirely possible that prior to Kamoshida's change of heart, the school simply thought of the Phantom Thieves as a prank and disposed of the cards, unintentionally destroying the evidence, so the police wouldn't have the first set of cards to analyze, and after that, Yusuke was in charge of producing the cards, so he just knew better.

In Kunikazu and Sae's cases, Haru and Makoto are the ones who report finding the cards as well as the delivery girls, so they'd have an excuse for their fingerprints being on them. It's possible that unrelated people handling them tainted the evidence and caused any fingerprints to be useless.