some hubs have a larger flange on the disk side as this make a stiffer wheel for braking

So does that mean one side of the wheel uses slightly shorter spokes? That seems like a hassle..

The majority of rear wheel builds will need shorter drive-side spokes so it's no more hassle at all.

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quite often on the rear, the idea of having differant sized flanges is so the spokes needed are the same length for each side. the differant flange sizes take into account the dishing of the wheel, so you dont need two differant spoke lengths for one wheel.
on the front if its a disc hub, the disc side flange needs to be larger so theres room for the mount. on a non disc hub, obviously both sides are the same.

just get new spokes you might not have the right size anyway and keep the two lengths split up

Spoke calcualation uses a complicated formular. Lets just say unless your swapping a hub for itslef there is no gaurentee that the spokes will be correct. Your best off talking to the wheel builder at you LBS and buying the correct length spoke.

Or order one from stif.co.uk or merlincycles.co.uk There wheels are wel built and resonably priced