It may be more cost effective to do them both at the same time....ie, if you have to pay per hour, removing the seacocks such that they can be reused, you may spend more in labor than simply buying new ones. This way if the seacock is damaged or needs repair you have the new one on hand, also the yard need not be worried about preserving the seacock in removing the thruhulls....I have seen them hack saw or hammer the seacock or use it as a leverage point in removing the thru hull, when they know that they do not need to save them.
If the seacocks are of reputable manufacture and materials, they can likely be reused, will likely need cleaning and perhaps lapping the surfaces as well as lubricating them. Some of the older gear is of far better make than the new stuff. If ANY have issues now, then replacement while you are out of the water is less stressful, than an emergency haul and hang to repair or replace.
Make sure that any leak stoppers currently in place, will work with the newly installed gear. Checking the backing plates and hull penetrations should also be done while hauled. Don't forget the electronic and engine thru hulls either.
Best of luck.