I think they should be. I downloaded and installed FSO SCP, then bought a video card, and cranked up the settings and the first thing that happened was a bunch of people telling me that I was missing this, missing that, etc. So I installed new beams, new 3d warp effect, new shockwaves, and new backgrounds. It would really help newbs to include all this stuff in an install, even if the high-res beams and shockwaves are the defaults, the lower ones should still be downloaded when the game is downloaded/isntalled, so people only have to decide to activate them or not. Presumeably, they could be in some separate/options directory where they could then be copied into the appropriate places.
Oh, I also ended up installing some modified tables, which were also user-suggested, to improve the sharpness/clarity of my explosions. So basically, the more stuff that could be downloaded automatically, initially, the better, I think.
There's a presumption of completeness when you get done installing a game that's several hundred megs. I had a lot of fun tracking the stuff down (seriously) but that's because I spend hours and hours a day staring at law books and anything else is high entertainment, plus I just like tinkering with settings and files. But for a lot of other people -- turnoff.