PA beat me to it really... Guns in a Zelda game wouldn't necessarily be a bad thing. I think the problem is most people's minds jump straight from "gun" to "turning it into another unoriginal FPS", and so they disregard the idea straight away... when really that isn't the case. Nintendo are all about experimenting, and though I doubt they'd actually include guns any time soon, if they did I'm more than sure they could easily make it work.
Right now, the series is actually already primed for them, to be honest... at least technologically speaking. On the surface, Zelda games appear to be from a medieval-ish period... but technology-wise they're actually already way past that. And I'm not just talking about the trains. As someone else said, guns wouldn't actually be that much of a technological leap... heck, something similar to gunpowder evidently already exists in Hyrule, and someone there already thought of packing it into a capsule with a fuse (bombs). However, already they've gone even further than that, as WW, TP, PH and ST show. One word guys: Canons.
Now before anyone starts with the whole "modern guns don't work exactly the same way as canons", that's not the point. The point is that someone in Hyrule thought of putting the existing form of gunpowder capsules (bombs) into an enclosed barrel and using the force created to propel a metal projectile. And, as that Bazooka in TP shows, they've already begun to modify it, make it smaller and less cumbersome. This indicates that with enough time, those original canons would eventually end up as something similar to our modern gun, presuming they kept up developing them.
A few people are also saying guns from the correct era would be too cumbersome compared to bows and arrows. Not to be blunt, but when has Zelda ever tried to be historically correct, or bothered about uber-realistic physics before? Nintendo could theoretically give the guns whatever reload time, degree of accuracy (or even the amount of damage the guns do) that they wanted (thus also restricting the gameplay and creating more of a challenge). Besides, this presumes the gun would be used alongside the bow and arrow in the first place- what if it acted as an upgrade, or replacement, or what if it was a hybrid of the two in the first place (or something crossbow-ish?).
Okay, with the "could guns be in a Zelda game" out of they way, onto the "should guns be in a Zelda game". Personally, I'm really not one for guns- in most games where it's viable, I always chose to fight with melee attacks rather than use the guns available. However, all things considered, one thing I do know is that if guns were in a Zelda game, they should still fit in with the context. If it's a medieval-ish era game, Bomb Arrows are just peachy, and guns need not be involved. However, if it's set in a closer-to-modern-times era, muskets and such could potentially work there, as long as they're not just included for the sake of it. And if, on the rare off-chance, the Zelda game's actually set in a modern-to-futuristic era, then by all means it would just make sense for modern-to-futuristic weapons to be included- including guns.
I'm not saying I want to see Link mow down hordes of moblins with a fully-automated machine gun (since obviously Nintendo would include restrictions to stop that, from the reload times down to the fact it probably isn't the most family-friendly thing in the world. And let's face it, being able to attack like that just gets so boring after a while, so if Nintendo had any sense (which they do) they wouldn't include that simply from a gameplay perspective in an effort to make the game, you know, actually fun). I'm just saying that guns, on their own, without changing anything else about the series (such as staying plain away from the various stereotypes that a game with guns brings) would actually be a perfectly sane idea, and wouldn't ruin the series by a long shot. Heck, there's a hell of a lot of worse things Nintendo could do to the series in the mean time.