I find Hyperion without SO not worth using at all. For what the costs of operating this ship are - both in and outside the battle - its all flash over substance.
WITH SO however it becomes so deadly that there's not much reason to not use the hullmod. 3 of those officered can destroy almost any threat in the game. Of course there's a caveat, that you need to minmax into the required skills so that the ship lasts long enough to do its thing before falling apart. This is probably the biggest problem, as it forces you into a very specific playstyle when using this ship. In my Hyperion run, I had to permanently shelf my Radiant, because out of all skills, the only one I could reasonably afford to drop was Automated Ships (Systems Expertise gives Hyperion more PPT and is a huge boon to lots of other ships, so it stays. Field Repairs isn't going away, as not having to restore a ship every time it gets a D-mod from being randomly blown up in combat is way too much of a QoL to pass up).
Another problem with SO Hyperions is that unless the battle was extremely short, they're already in red CR after just one engagement. If you rely on those and are faced with two engagements back to back - you've got nothing to defend yourself with.
In the end, despite the caveats, the ship is just begging for SO. If you're not committing to that, it's absolutely not worth the hassle. Its destroyer-class stats, sub-destroyer-class weapon mounts and its gimmicky system are not worth the 40% CR per deployment, 30 maintenance cost, and 15 DP, unless maybe to capture a point and then immediately retreat it.