You talking actual skirt steak or something like sirloin or flank steak cut into strips?
I'm all for experimenting and letting us know how it goes, but I don't think skirt would do too well in the smoker. At least it won't be prepared in what I consider the traditional fashion. To me it just seems like overkill for something that is so easy and fast to cook in the traditional way. And if cooked over a good and hot mesquite grill, it'll be nice and smokey and juicy.
I was born and raised in deep South Texas--arguably a primary source of what we consider fajita in america given the border influence. True fajita being beef skirt steak. Before it became popular it was considered a tough, trash cut of meat; only eaten by po'folk, ranch-hands, and such. People ate it b/c it was dirt cheap. Kinda like brisket way back when, if you think about it. When I go back home I still seek out and enjoy some well prepared "cuts" (organs) like lengua (tongue), molleja (thyroid), tripas (intestines), and goat. When done right this stuff is awesome! Just don't tell my gringo wife what it is
All that being said, I think the best way to do fajitas is on a HOT mesquite-fired grill. They're thin so they don't need that much cooking time; maybe 5 - 8 minutes per side depending. In true SoTex fashion, I nearly always grill up some green onions that have been marinated in regular old cheap italian dressing. Just wash, trim the roots and some of the green. I like to keep lots of green on mine. For reference on cooking time, I usually throw the green onions on first as they take longer than the meat. Sprinkle with a little salt if desired and serve with good lime.
As ECTO1 said, a bath of a few hours to overnight in italian dressing is one of the best marinades for the fajita too. If you get them untrimmed and unseasoned you'll want to trim some of the fat off that one side.
Personally I like to keep serving simple and what some may call "Rio Grande Valley-style". Just some meat (cut against the grain, of course) in a tortilla that's been heated [on the comal (cast iron skillet) or a grill] topped with fresh lime juice and some finely chopped raw onion and cilantro if you got'em. Green onion and a pickled jalapeno on the side. Beans either refried or charro help it all go down. Man, now I'm getting all homesick (and hungry)!
Again, that's just what I grew up on and what I personally consider properly prepared fajita. Go with your gut and let us know how it goes. Might stumble on something good! Whatever you do, watch out for over-drying the meat as dry, tough, and overly salted fajita is a major bummer.