Using my system, the turret missiles come in at something like Cr12000 average- you can cut features but it’s not good to.Something like that. The "miniature fusion generators" used in PGMP and FGMP type weapons could be an inspiration here. Use those either to power grav thruster or a small fusion rocket.
Unfortunately, that leaves little room for SS3 unless you massively rework it. I like the idea of a missile design system, but I think missiles in CT need to be re-thought completely. Also unfortunately, if you want to keep things proportional, that would mean missiles would probably cost Cr 50,000 and upwards. Then again, that could also be considered a feature. In Book 2 combat, missiles can be fairly devastating (especially against typical low-acceleration opponents).
Vague idea for IMTU is a turret missile massing 250 kg (should still be small enough to move it through spacecraft corridors if broken down into major components), costing Cr 50,000, and a bay missle ~4 times as much.
Bay missiles come in at Cr 150000 or so. If you add the nukes it’s Cr100000 plus for the turret missiles and MCr1 plus for the bay missiles- very much like the supplement.
This is not surprising to me, they obviously tried to hook up Striker to HG, most notable with the lasers.
I went ahead and worked out KEAP vs HEAP warheads- the bay missile HEAP comes in at pen 58, just shy of the initial armor level and easily punching through classic unarmored ACS. So again they definitely had shaped charge warheads in mind- or at least the regular warheads were KEAP and the souped up shaped charge ones were HEAP.