Yes, but the presence of three or so poorly marked emails among tens of thousands of them over four years does not do a great job of establishing intent - as opposed to this case, where the Booz employee was found with tons of presumably clearly marked classified documents.
Even the destruction of evidence is illegal. The State Department ordered her to return all emails, she had staff (incidentally without security clearance) delete tens of thousands of them.
The state department has recovered emails sent and received to her (for official functions) which she failed to turn over. This is in the FBI's report and also in the private lawsuit filed by the Republican group.