who actually wanted to know my thoughts on this. It may well be TL;DR for pretty much everybody else.
First of all, a disclaimer. I don't actually know anything about propulsion, advanced mechanics or have even anything more than the most basic understanding of physics. I am not
smart in this area, so prepare for some possibly very stupid theories on how Star Trek engines work.
What sparked this post initially was the question of why there didn't seem to be an engineering area on DS9. My simplest theory on this is that since a space station is not actually meant to go very far in any direction, it doesn't need a huge section for propulsion alone like a starship would. I am assuming here that a large part of what goes on in engineering is centered around making the thing "go". I know it has other functions, but perhaps due to size and ship design or even just practicality, I suppose it makes sense to have it all in one place.
DS9 is not only a completely different sort of beast, it's also huuuuuuuge. The Enterprise is just one of at least 6 full-size vessels able to dock simultaneously at any given time. If we ignore design entirely for a moment, it's actually possible that DS9 has not one, but perhaps dozens of engineering sections, all of them easily the same size as the one on the Enterprise, just to produce enough juice to keep the thing floating or whatever. This would not surprise me at all, since it was very clear in the first episode that O'Brien getting the job of Chief Engineer of DS9 was a big step up for him.
DS9 also has a lot of things starships don't. Docking pylons, storage bays the size of a small village, a frickin' strip mall! I have no idea how much energy this stuff would require to keep running, but I imagine it would be a lot. DS9 does have a central core, but it's fairly vague what actually happens there. Does it produce energy? Is it where the big red "off" switch is? Is it merely a junction for all the Jeffrey's Tubes? Nobody really knows. The only thing we really do know is that blowing it up would be bad.
Also, depending on when in the series we are, DS9 has proven capable of:
-Keeping between 2 and 7 thousand people alive and happy at any given time.
-Holding off an entire Klingon fleet.
-Holding off a Dominion fleet (!!)
-Producing effective shielding for an area maybe 50 times the size of the Enterprise.
-Churning out a frankly massive
amount of mines to block the wormhole, so one can assume the capacity for production is also fairly huge.
So the sheer amount of power needed is already mindblowing. For practicality, it makes sense not to have it all in one place, so if something should break down it will only affect part of the station. We fairly often hear of the pylons breaking down, so I assume they at least have their own closed systems. I also like to assume that several other systems run independently. Like weapons, transporters and life support. Considering some of the juggling they do with technobabble through the show, this seems highly likely.
The arguments above are pretty much exclusively based on practicality. If we move on to design, there's a whole different level to consider.
DS9 is Cardassian in design. And not only that, it wasn't originally even a space station as such. It was an ore processing plant. It was never built to be a major defensive point, a diplomatic nexus or even to be all that comfortable to live on. It was full of slaves and grudgingly stationed military. (Apart from Dukat, who seemed to love it there.) So the fact that eventually thousands of people seem to live quite happily there is an accomplishment in itself, and it's hardly surprising that the steps taken to keep the thing going, for something that was never its original purpose, would involve some heavy re-designing. If nothing else, O'Brien seems vastly imaginative about how to keep things running. For all we know, the smattering of engineering sections could be mostly just him pulling a Frankenstein to hold everything together and make the Cardassian systems work along with the Federation ones.
Add to that the fact that we don't actually know the logistics of Cardassian engineering, and we're in a completely different ball park. Perhaps whatever makes Cardassian systems go round can't actually be kept in one place for whatever reason. Maybe the placement of the systems was originally just for decorative purposes? We can't deny that there's something artistic about the design overall. There's not a lot of information to back up any of these theories, so really, the sky's the limit with this.