Have you ever worked on or seen a FMECA? Even for a simple system, they are a truly stupendous amount of work. A few years ago, I reviewed one performed by someone else on a relatively complex system (four electronics racks, plus some ancillary equipment), and reviewing it alone took about three full-time months. I don't know how long performing it took, but it was at least several man-years dedicated, plus several more intermittently from the actual designers. Multiply that by the number of comparable systems on the Death Star, and it's likely that literally hundreds of thousands of man-years which would have to pour down the drain just for this single engineering task.
Further, when designing anything, you're playing a numbers game. Of course there will be things which could destroy your system. If you throw a handful of rocks at your laptop, there is a possibility that they will land on the keyboard in a way which correctly enters your password, calls up a command prompt, and types in "format c:". How much time should you spend "fixing" this exploit? Should you even document it? Should you even consider it? (my very rough estimate is that doing so would increase your FMECA time by at least two to three orders of magnitude).
Finally, even with small projects (like a DVD player) not everyone is an experienced senior engineer. You involve junior engineers because you need the help and because you need to give them experience (or else this generation will die off, and you'll never get a Death Star 2). This, incidentally, is one of the reasons that power supplies are so failure prone in most consumer devices: Power supplies are the part you can most safely assign to the least experienced designer.
So, what does the actual engineering analysis look like there? You probably have a junior guy looking at the exhaust system. If he's good, he probably comes up with something like "sudden over-pressure" as a failure mode, and shows that the next-higher level effect is feeding a pressure spike back into the core (many unstated and charitable assumptions about architecture there). With really, really, good analysis, that probably rolls up to some sort of critical failure. Junior engineers are excitable, so he probably assigns that a high likelihood. Let's assume he assigns it one high enough to push it over the threshold of "worth fixing." The lazy way of fixing an over-pressure in a straight pipe (especially if you don't believe its really a problem) would be to widen and straighten that pipe. 81
So now, instead of a one-meter opening, it's a two-meter opening. Problem solved. (And if you're the overall system architect, this is a great place to put your thumb on the scale to create a vulnerability).
But maybe some survivability or safety engineers come along afterwards. This is a military project, after all. They're going to brainstorm a bunch of stupid edge-cases ("but what if the Death Star flies through a sun?"), but for everything real they're going to look at the FMECA failure modes. So, maybe they see that there's a place where "sudden over-pressure" causes a system-level problem (which already required quite a lot to go right), and maybe they think of proton torpedoes at that point. They probably do some pseudo-Bayesian analysis to find the probability: given that the Death Star is hit by a proton torpedo, will it hit this vent? And that probably looks like (surface area of vent)/(surface area of death star), because this thing is trivial anyway, and because its all classified you're looking at random chance, not deliberate action. But assume they decide that this one-in thirty-seven-billion chance is too high. How do they mitigate it? Well, maybe shield the vent. You could put a grate over it, but that's not ideal (the failure mode is "sudden over-pressure." What does that mean for an explosion at the mouth? Who knows!). But there is a trench nearby, so it's trivial to re-route it there, so the exposure is also limited to a much smaller range of attack angles. If you're still super-worried about it, throw a few extra turbolaser batteries around nearby and call it a day.
All in all, it's incredibly unlikely that this was the only such flaw. It's the flaw which was called out in the movies, but there were probably a half-dozen ways to mess with the superlaser emitters just right and blow the whole thing up too. 963