If you're recording for YouTube delivery, then I think whatever is easiest would be the best choice. YouTube compresses the audio anyway. You'll lose more audio quality then than what you'll notice from recording at a higher sampling rate (probably imperceptible). Don't sweat it and go with the easiest way for you.
As you allude to, 48 kHz is the standard for video. I have absolutely no idea if this goes for youtube videos too and how that all ties together.
I'd probably record via analogue outs into a session at 48 kHz, for simplicity's sake. No reason to record at higher sample rate and then downsample, I think.
I have absolutely no idea if this goes for youtube videos too and how that all ties together.
Youtube accepts 48KHz or 96KHz. Just an FYI :-).
96KHz on PooToob?
Now that's overkill if ever I heard it... not that I'd hear it at 96KHz... 
Try it out. You probably won't notice a difference.
I guess my real question then is, what sounds better-
Digital in at 44.1khz then convert to 48khz for the video or
48khz analog?
There shouldn't be any difference if you have halfway decent converters. If you don't, go with the spdif. But I doubt there's a problem.
I purchased a used Behringer SRC2496 off Ebay, and connect it via SPDIF in between my KPA and Roland interface. It can convert my KPA SPDIF to any sample rate between 32kHz and 96kHz, in realtime.
Yup. I reckon the line outs sound superb, pristine, awesome and... perfect.
I get the feeling that many, by default, assume that the digital output will by its very nature yield superior results.
In the real world, however, I doubt very much that this is the case; if there is a difference, nobody would hear it IMHO.
