Im pretty sure the 3I would discourage these sort of fixed defenses, as they make it much more difficult for some Imperial Navy or other to keep member worlds in line if necessary.

On the other hand, I can definitely see their uses for certain worlds during the Long Night or similar, especially because I think it's canonical that the Vilani didnt have meson screens at all.

They could also be worth having if you want to discourage small raiding forces but, for whatever reason, dont want to use SDBs.

Im a little unsure why a deep meson site is a better option than a very big SDB - the size of the caverns needed for the Deep Meson Site should show up on gravity and other sensors, as should much of the support equipment, and the sensor systems feeding them data are still vulnerable to orbital bombardment even if the site isnt. Im not even get to the need for radiators for the power requirement for them.

Basically, IMO a buffered plantoid in orbit with really thick armor gets you most of the advantages of the deep meson site, and the tunnelling should be simpler, and with Trav technology you can move it at one gee. 

Ian Whitchurch
I can see Our Heroes being contracted to try and find a Deep Meson site on a world that seemingly had one during the Second Imperium, but the records were lost between the second and third ...