On my old guitar, I got the Duncan hot rails in the neck and liked it. I'm getting a new guitar soon and I can't decide whether I want another HSS or get an HSH this time around. Is there any big difference that I'd be missing in the neck if I didn't get a full size (probably an Air Norton)?
Nah, there are plenty of excellent choices in single sized humbuckers, such that you would be fine getting another SSH guitar. Some would argue that the full size humbuckers sound better, but I haven't noticed.
I'd say a bucker's good for the bridge but a single is better for lead is anthing, so not a bad decision for the neck. If you're doing really high-gain (like, death metal high-gain) solos then a bucker might be worthwhile, but anything short of that a single will suffice, if not excell.