I think you're overestimating the empire's ability to accurately report on battle losses and disseminate info in training. It's an expansive galaxy. We've seen them fail at this before and even if they did it, individual actors can still make bad calls or forget in the moment. You can make the same argument against the anti-trator beam chaff cannons, if the empire navy learns from this encounter and treats every tractored ship as if they have surprise chaff cannons they wouldn't be effective again. So in that sense the chaff cannons are not more practical than the side beams because both rely on the element of surprise / the empire underestimating you.

A wing of fighters that wants to kill the Fondor in open combat will win every time, it's not a ship built for 'traditional' naval combat in this setting. It's a ship built to look like a regular cargo hauler until suddenly it's not, long enough to jump into hyperspace. If this is the only time the side-beam weapon works, it will still have been worth installing because it helped Luthen escape a fatal (one way or the other) encounter.