As far as his security clearance goes, he no doubt has some, but in S05E21: "Soldiers of the Empire" Kira stated she needed Bashir OR Dax as the intelligence officer because only either of them could fill that role with Worf off station. That directly implies O'Brian lacks their clearances, which, honestly follows military logic of Non-Coms.
That being said, they actually considered O'Brian a non-com for a long time. In S04E02: "Family", Worf's adoptive father identified (magically) as a Non-Com. Roddenberry with his military background probably considered O'Brian a non-com for a long time but simply didn't put much thought into his insignia. I'd suggest from the time we saw him as "Chief", he was considered a non-com from that point on.
Really, it was on S04E12: "The Wounded" that messed us up with O'Brian. Everything in the future and before made sense until we found out he was a tactical officer on a Light Cruiser. Tactical Officer on something like an Escort, still makes sense, but a Light Cruiser? No.