Is it more cost-effective to sell many items of poor quality, or fewer items of higher quality that have been repaired together? Does the answer change depending on the item? Does it change depending on my repair skill?
You should repair items before selling them, rather than selling many cheap weapons.
There are two reasons for this:
Once you hit a repair skill of 90 and level 14, it's worth picking up the Jury Rigging perk just so you can merge vaguely-similar weapons together (and convert the cheaper weapon into a higher quality on the more-expensive weapon).
*This depends on your skill, of course. I don't have numbers to back me up, but if your skill is below 25 or so, you may lose money. (But you'll still make more money-per-minute-played, because you're not trudging back to town as often.)