I've almost always preferred logos. I don't know why, but I think it goes back to my love for the late 80's Ibanez'. Not the RG's so much, but the Radius, Saber (S series) and Power. They all had IBZUSA pickups made by Dimarzio, and I just liked the little finishing touch the logo added to the look. Of course, anything vintage looking I prefer no logo, but only if it's REALLY vintage looking. I can go either way on a Strat, but if it's a butterscotch tele then no logo for sure. H/H guitars are a toss up for me. I usually like logos even if it's an SG or Les Paul.
I don't have an answer for you on the logistics of the logos, whether there's a charge or how long it takes, but if you call in to Customer Service, they can help you. We can definitely do it for you, provided the pickup hadn't been modified and no longer an acceptable "Seymour Duncan" product. In other words, we probably wouldn't logo someone's hybrid, or a non-Duncan rewind, etc.