Well, goodness knows I only mess around with RAM or ROM manipulation for experimental purposes, but as for glitches.. whether the developers intended them or not, they are a part of the game.
Personally, I couldn't even tell you how to play Metroid Prime without scandashing to get the Space Jump first, anymore, and I know a lot of Super Metroid players who don't remember how to not mockball (I'm not quite there yet, if only because it still takes me about a dozen tries to get it to work).
If a developer is able to and chooses to remove glitches in a later update or sequel, that's fine, of course, but sometimes they won't (or in the case of older games, can't).
Fighting games in particular wouldn't be what they are today if someone hadn't found an exploit in Street Fighter II that allowed them to shorten certain attack animations and thereby get in even more attacks (a concept we now know as "combos", which has expanded far beyond the scope of its originating genre).
Other examples of glitches that became so ubiquitous that they were deliberately incorporated or left alone in later games and updates include the Roman Cancel from Guilty Gear (now a staple of the series, which even added a False Roman Cancel just to throw other players off) and Mutalisk Stacking in StarCraft (rather than find a way to prevent players from doing it, Brood War added a selection of new units specifically designed to counter the technique).
And then, of course, we have things like Wavedashing which was deliberately left out of Brawl.
But my point is that glitch abuse in and of itself is not necessarily a bad thing, least of all in single-player games like the bulk of the Metroid franchise.
I will, however, agree that when an exploit in a competitive multiplayer game creates a serious imbalance, then it should be fixed as soon as possible.
