Missile bays are going to be of VERY limited utility against deep site meson guns. Especially if they use arrays of redundant passive sensors connected by meson comms.
The ways you stop the deep site meson guns:
1) Infiltration/Espionage
2) Meson guns from space
3) scrub the surface with pattern bombardment - Missile and/or meson.
note that 3) isn't an option if one intends to use the planet and its infrastructure.
recruit an team of eccentric soldiers with severe discipline issues, and prone to character clashes, deploy them in secret behind enemy lines...( of course they run afoul of traitorous allies, and escape through clever ploys) then at a climatic moment they strike using inginueity and daring...
you know I think I just described the plot of a movie....and a certain 1970s
sci-fi episode...