I took my T9 out to the new triple last night with two subsurface launchers on the outer medium hardpoints (medium mining laser in center) and can confirm your observation with the Cutter: "the missiles will not hit the deposit if you are centering the reticle on it."I have not suggested neither the type-9 or the Cutter because of their lack of agility. I may do some tests in the type-9 or the Cutter later to see if their collector numbers and cargo capabilities can offset the lack of agility.
However, I used fixed missile racks and not turreted - perhaps this could help as I noticed in your Cutter build you also had fixed. This made it very difficult to adjust for aiming. Coupled with the general lack of agility, I had to pass on many subsurface deposits on rotating asteroids. I also went through both banks of ammo missing terribly and had to synthesize ammo to finish up.
But when I could hit, the mining was good. Might try a test run with turreted missile launchers to see if that fixed the aiming reticle problem. I have A-rated un-engineered thrusters, so engineering might make some (small) difference.
Thanks for the build info.