Perhaps it's because the weapons they'd use to handle an ambush are drawn from their thighs and behind their backs. I'd think it would also give them a uniform running profile so that there is no 'best moment' to attack them. If you run with your arms swinging there will be moments when your hands are completely out of position. Especially if you have, say, a left thigh shuriken holster and a right shoulder sword draw then you will constantly be creating a moment where you can easily draw neither weapon due to arm swing. Thirdly it allows you to draw and throw weapons hidden in your sleeve without the delay of needing to swing your arm back.

I suppose it could also be an artifact of chakra assisted movement. A proper calisthenic running style might conflict with getting the best results from a run that relies more on sticking with chakra and explosively releasing it for a 'push' rather than the rounder motion of running based off pure athleticism. Perhaps it also helps their moment to moment balance by keeping their center of gravity near constant rather than allowing it to sway, that would theoretically allow for faster, tighter reactions and evasions.