Is sound quality at all effected by using pedals before the interface, as opposed to recording a clean sound and applying effects in the DAW?
I am using a Scarlett 2i4 interface.
I wouldn't record using FX unless I was very sure about the end result I wanted and how it would sit in the mix, just to leave my options open since you can't go back and remove the FX. On the other hand, if the FX are an integral part of the performance then it might be a good idea to record after the FX. Sometimes the performer might hit a 'sweet spot'that's hard to recreate later or simply change the controls as part of his performance.
If you have a spare channel (if it's a mono source like a guitar) you could use one channel for dry and the other for wet recording - even just to 'keep a note' of the sound you're after when you add the FX later.
The sound quality difference itself is quite hard to make a guess on, but my best guess would be to run the lowest impedance source through the FX. That should be the Scarlet. I think mics and instruments almost always have higher impedances. This is if you run the dry instrument/mic through the outboard FX. If you're planning to use software effects, then it's too broad a comparison to make. The quality will depend on the quality of the effects used, both outboard and within the DAW.
Attitudes on this topic are going to be mostly religious, punctuated by a few facts. Some of these facts have already dribbled in...as Simon mentioned, some pedals may introduce unwanted noise. And as Schizo posted, you can opt to keep a clean copy of the track.
Another fact I'll throw in is that not all effects are created equal. For example time-based effects like delay, reverb, chorus, phase, flange, etc can be locked to the tempo track, so in some circumstances, it may be better to introduce them at the board/in the software, rather than have the guitarist bothering with their own effects. Meanwhile, effects a guitarist identifies with as being part of their "sound" are reasonable to keep in place as pedals, such as distortions, compressor/sustainers, EQs (some are groaning I'm sure), etc. Moreover, as a guitarist myself, I want my whole damn rig in the capture chain...my amp, my cab and its speaker response, my pedals. And I'd be shocked if this wasn't common.
You get interesting collisions within this philosophy when a guitarist uses a time-based effect as part of their signature...I'm thinking of U2's the Edge, who makes considerable use of delay. Or Van Halen, who at least early on applied alot of flange.
On the final analysis, we can debate this all we want, but a recording is a creative product that happens when you mesh musicians, tech/engineers, and/or a producer together, and there's no rule that says you have to stick to one recipe. Consider that Mutt Lange produced both AC/DC and Def Leppard. And he used very different approaches with those two bands. AC/DC was all about the sound and natural energy of the room, whereas Def Leppard was layers and layers and layers of production right at the board.
In terms of the sound quality of a particular effect, I would opt to use pedals instead of your DAW's digital effects. For me, I've noticed analog effects to be much more pronounced and soothing to listen to - it's hard to say precisely why this is.
Also, while it's true that your pedals' effects will be permanently imprinted, is this really a bad thing? I would rather be able to move on from a great sounding effect than constantly twiddle with my DAW's digital effects until the end of time.
Or - you could do both. Layer a clean track with your digital effects on top of the track with your guitar pedal effects. Just do what sounds good, man.