These indictments are the result of a massive counterintelligence operation spanning many agencies from several nations. In this case specifically, the AIVD (Dutch intel) hacked the GRU offices where a large part of the hacking was carried out and managed to exfiltrate significant amounts of evidence including CCTV security footage of GRU officers coming and going [1]. The evidence proving the crimes for the purposes of a conviction will be made public but unless lawyers for the defendants come to challenge the warrants and get them unsealed, the evidence that led to the public stuff will likely stay secret for decades.
[1] https://www.volkskrant.nl/wetenschap/dutch-agencies-provide-...