One would think that the Oberth is very modular to begin with, even without swapping the lower hull or pod or whatever. Regular changing of all the major sensor elements seems the only way the design could remain valid in the science role for a century.
We could for example assume that the slightly inset ring atop the saucer, around the bridge, features sensor modules covered by suitably radiation-transparent panels. We could then assume that any one (or two or three) of the modules can be replaced by a phaser turret, and a couple of others with the required targeting hardware, in case Starfleet feels that this particular ship is going to face the risk of combat. The ship probably wouldn't have enough power (or enough capacity in the power transfer systems) to fire a great many of the modular phasers, though. It would be a bit similar to how mercantile ships are armed in wartime: only the lightest guns can be installed without buckling the deck plates. However, while a merchant ship today could theoretically ship dozens upon dozens of light AA guns, which each have their own "power source"/ammo, an Oberth wouldn't similarly benefit from filling all her berths with Type 4 phasers.
Torpedoes would be much more difficult to quickly install or retrofit to the design, I'd think - the equipment appears to be very bulky. I actually assume that most Oberths don't have the capacity to launch either torpedoes or probes, as there is no suitable forward opening in the model, nor is there any sign that a ship of that class would have fired either type of ordnance during the course of the shows and movies.
To be sure, there is the motion control rig hole at the aft end of the lower pod. Perhaps that one is an aft-facing launcher? Would be nice, really, as an Oberth in battle would usually be flying away from said battle as fast as she could...
Generally, I'd think there would be plenty of roles in Starfleet for completely unarmed ships, too. Even when fighting the Borg, an unarmed science ship might do her part, using superior sensors to try and defeat the Borg advantages and second-guess their adaptation routines, then relay the intelligence gained to the armed combat vessels.
Timo Saloniemi