Maybe they’re compromised but data seems intact, as in it’ll be irresponsible to keep serving on the Internet but most of it are probably not maliciously altered?
Yeah, it's pretty common for hackers to upload backdoors to random web sites when they can and exploit them at a later date. If we're talking about a full server compromise then I wouldn't use those downloaded data for anything except for analysis/archival purposes, unless it's been thoroughly cleaned first.