Well, bug or feature depends on how you like it. Right now I'm building on strict HG, so it's a feature. Once I've got it working, I'll change it to the house rules I use, which treat that as a bug.
OTOH, even using house rules where spinal meson guns are not so devastating (usually by allowing meson screens to act as "armor" against meson gun fire) the type of damage that meson guns do is different and more lethal than the damage from missiles.
Meson guns roll on the Internal Explosion table while nuclear missiles roll on the Surface Explosion table (both also roll on the Radiation table, but I'm ignoring that for now). Thanks to the heavy armor found on most capital ships, rolls by missiles on the Surface Explosion table are usually shifted up to become Fuel-1 or Weapon-1 hits or just "No Effect". However, even if you allow meson screens to act as "armor" and shift meson gun damage rolls upwards on the Internal Explosion table, you still get a damaging assortment of potential results: Jump-1, Power Plant-1, Computer-1, and possibly worst of all, Screens-1 or even Screens-2. All of these results are much more important than scraping weapons off the hull or making leaks in fuel tanks.
So, even if you're in a universe where meson screens are more effective (like TNE, for instance) meson guns still do a qualitatively different kind of damage, a kind that is much more likely to lead to the destruction or capture of the target, rather than just forcing a disarmed retreat.