I own a couple Nagasawa track frames. You won't fit more than a 22 mm tire under the fork crown of a Nagasawa, and at that point you will have trouble getting clearance to fit a short-reach brake (if you're going to use one, of course). Plus, the front end tends to be pretty steep and stiff -- not very comfortable on the road. The paint finish is beautiful, but whatever he uses isn't as tough as some of the epoxy finishes that American builders use. Plus you're stuck with a traditional non-sealed headset that needs constant maintenance if you ride it in the wet and with quill stems.
Nagasawas also come with around a 5 cm bottom bracket drop. Road riding doesn't need anything more radical than a 6 cm drop, and perhaps even 7 cm. (I've never scraped a pedal on a fixie with 165 cranks and a 7 cm drop, although I am using low-profile pedals -- a 6 cm drop would give you clearance for any pedals.) Now that 5 cm drop makes the top tube rather high against your anatomy, plus it makes the bike noticeably less stable on the road. Nagasawa doesn't let you specify specific dimensions like bottom bracket drop -- he asks what track you're riding and designs for that track.
Nagasawas and Vanillas are both amazing eye-candy. Both ride superbly well. From an artistic standpoint, they are almost polar opposites -- one is completely traditional with touches from a 1966 Datsun, the other is pure rococo. Both can and should be ridden. I might say it's criminal to drill a Nagasawa fork crown (he'll do it for you in a new frame, but only if the geometry and such are basically aimed at a road fixie -- you can't get a drilled fork any longer with keirin geometry).
I'd suggest you look at Spectrum Cycles (Tom Kellogg). They make absolutely gorgeous track and fixie frames with some of the finest lugwork and finest painting out there. Tom and Jeff know track frames like nobody else in America, they deliver in 2-3 months, and you get an incredible bike. You should also take seriously the suggestion above about Kalavinka -- I have a couple Kalavinka frames and can attest that Tanabe is very easy to work with, delivers on time, has great product for the price, etc. I think the Spectrum is a bit nicer, although you won't get the nice kanji graphics that way. Still, avoid the long wait lists and go with someone who really knows bikes. Kellogg will guide you through the design process better than anyone else.