It's actually quite a difficult subject to consider how to change the basic 'magic effects', I said they could (should) be removed with this I was aiming at the ridiculous ones like self loading shotguns that never need you to reload until you run out of ammo, or the assassin gun that does 50% more damage to humans, I found that on a Synth legendary. These sort of examples are the ones I class as just damn silly, TBH I actually think they are almost laughable and in some degree insulting to the players intelligence.
But items like a stealth suit (or shadowed armour) that have say 25% increase in stealth literally must have those effects because without them you could not do a 'real life' hid in the dark type thing, if you stand in the shadows in dark clothes in real life someone may pass you by and not notice you? In a game the AI can only (so I believe) allow that to happen if the maths of stealth bonuses stack up enough to duplicate a real life situation, NPC's from what you can experience in game can see you as such in the dark just the same as daylight. They see you to shoot at you in the dark even if you cannot see them, so the 'stealth bonuses' give your character the 'magic effect' of not being seen so easily?
IMO opinion those Over the Top 'Magic items' should be removed and the sensible 'magic effects' needed to duplicate 'real life' should stay, things like a special armour that increases sniper damage, is that really possible??? I must admit I scrapped the never reloading shotgun as I felt it was just too stupid an idea.