I've used Cheat Engine for years on steam games and am still in good standing with VAC. Although, I've never used it with games where it would be a problem to use it on, i.e. multiplayer games. From my experience, it seems fine to use as long as you don't use in games where it might impact other players. Also, in most cases, Cheat Engine wouldn't even work in multi games where values are checked server-side for validation. The user values would likely be ignored and immediately revert to the actual one according to the server.
If you wanted to be safe though, you could always switch steam to offline before jumping in.