While I haven't done a Du in...three years, I used to do them a lot. Is the course flat to lightly rolling? If it is...just use your pedals with toe clips. If it were longer and /or hilly, I'd say use the bike shoes and pedals.
My transition times were always under 30 seconds when I went with Pyro Pedals or toe clips for the short stuff.

Correction: I guess I never posted the results of the experiment. If you read my OP in the thread above, you know the background. Well, my Dad's transition time for both transitions was 28 seconds, his bike time over 10 miles was 28:43 over a flat course. Mine for T1 was 45, they didn't get T2, but my bike+T2 time was 28:02, and that included a minor wreck because a volunteer told me the wrong turn. We both won our AG's (I was 20-24, he was 50-54).

I would say its dependent on what your goal for the race is (are you going for an AG win?), and where you're strongest. If you are a killer bike rider, use the clip ins, as it will give you a greater benefit. However, if you always struggle in transition, just go with the cages and hammer.

I know it was a highly un-scientific experiment, and it doesn't help that I wrecked nor got a bike and T2 time separated, but I hope that helps.