Well, that has always been the case with any weapon. Magic will still be more powerful than a bullet.

I guess it is more about aesthetics than logic for me. The technology would dictate the kind weapons (laser pistols, light sword, remote, controlled bombs), navigation (motorcycle, hovercraft, jetpack), puzzles, (hacking, pushing boxes will never go out of style).

Enemies can still be monsters, they don't need to be robots.

Magic does not suddenly evaporate with the development of technology. They can be separate abilities, or integrate mana style into objects.

As far as Ganon goes, whatever. If the Star Fox team can fuck up a giant ape with an arwing, link can handle a big ass hog with a gun.

It could be framed in a time where magic is largely forgotten.

Zelda and Link are frozen in time due to some great cataclysmic event in the past that left Hyrule in ruin, and thousands of years have passed, where the remaining people built over the remnants of the past and have entered into the industrial revolution, with dark and intricate, smoggy towns.

Zelda and Link they to make sense of this world, that ridicules their speech, their clothes, their mannerisms, but is shocked by their physical and magical prowess.

Zelda's magic is weak at this point, but it's enough to inspire hope in the bleak factory workers of the future.

Link uses his old gear combined with new gadgetry to navigate the steel jungle of the era, and find clues to the source of great cataclysm that happened all those aeons ago.