The warning is, most likely, there because the game was updated on Monday. Mod creators will have to update their mods to the new version before it goes away. However in most cases your mods should still work fine as it was a patch with mostly bug fixes and not content changes.

In this case it's more of the mods not being their up-to-date versions. They did update through steam, yes, but apparently the ones in the launcher are not the updated versions of the mods.
Game might work just fine though, I just haven't given it a spin yet. (Though I'm unsure if the game even lets me play)