Skate shoes daily? I would say nah, the opposite... Just look at weight lifters who use converse all stars. The flatness is great for letting all those micro muscles, tendons, etc, in your foot get activated. Wearing them regularly would generally create a more active foot, more balance and stronger muscles.
As for actually jumping down shit with skate shoes on, if they have no cushion at all then obviously your feet are going to take a beating. You can combat that by wearing good shoes or insoles, maybe even do some exercises to keep your arches strong.
Flat feet are mostly genetics, from serious foot injuries causing weak arches or from being such a fat fuck that your feet flatten out under your own weight. I have high arches and cannot relate to anything flat footed but I hope this helps dawg
Like i have said before, if you're 360% serious, then go see a foot doctor and not the slap message boards lmaoo