Of course it makes sense. O'Brien's an experienced NCO with at least 20 years in the service. A junior officer would be wise to learn from experienced NCOs, and would find it a bad idea to try to order one around.
No it doesn't actually. I became a Platoon Leader at the age of 22 with a Platton Sergeant that was pushing 40. I took full advantage of his weatlh of knowledge but the platoon was still under my command.
I'm not saying it would be wise to order O'Brien around like he's a private or anything but having officers REPORT to him is incorrect. An officer would be more like an administrator anyway than a hands on kind of guy. More of a director of what needs to be accomplished and where to direct manpower. I would definitely rely on O'Brien's expertise when making decisions especially if I was an ENS but I wouldn't be reporting to him. When in charge, be in charge is drilled into officer's heads at a young age.
Then again this is Starfleet so who knows what kind of crazy chain of command they have.
Which ensigns reported to O'Brien? Nog? Maybe a few ensigns in the early seasons of DS9? Were they really reporting to the Chief, or were they learning something from him?
We saw lots of officers doing hands-on work in Star Trek; Picard loved to see his junior officers getting hands-on experience with systems. Sisko probably did, too. Or, the ensigns and lieutenants that were seen "working" for the Chief were there to learn about Cardassian systems - a great chance for Starfleet engineering officers to learn more about Cardassian engineering practices. Maybe some of them were intelligence officers?
Star Trek really didn't introduce enlisted characters until they had settled on O'Brien being an NCO. After that issue was resolved, O'Brien had plenty of enlisted folks under his authority, both on the station and on
Defiant, and we didn't see many incongruous situations with ensigns and lieutenants taking orders from a Chief.