Are there still active modscenes for newer games? Minecraft is the only one that really comes to mind.
I suspect there's another problem with mods today: asset production. In Half-Life's day even I could hack out a semi-passable player model in a day or two. Nowadays, producing assets for games has been made dramatically more complex. In short, you really can't find a lot of people willing to produce that quality and complexity of art for free. The size of teams required to put anything together, as a result of this, has also put a lot of things beyond a mod team's modest reaches.
I think that's why a lot of the indie excitement is around casual and "low-fi" games like Minecraft. Assets have always been a major blocker, and when you embrace the fact that you're not AAA, you have a better experience with it.
I haven't really checked moddb.com since Unreal Tournament 2004 was the big online game, but it seems to be going strong.
Seeing the success of Counter-Strike, and the mod-mania of that era, got me interested in modding, where I was first exposed to the complexities (and math!) that "real" software entailed.
From there I went on to write some standalone, small games, then went deeper down the C++ rabbit hole which helped me get my first software internship. The rest is, as they say, history.