You've introduced huge numbers of additional variables, but also you now have multiple stutterwarping vessels. An oddity of stutterwarp is that stutterwarping vessels struggle to communicate with each other. Signals are sliced up and for meaningful communication to occur a whole lot of stuff has to happen with neither side unable to maneouvre. Typically, if you really want to "talk" then all ships need to disengage their drives. If you can't do this then (per Challenge 30)::
"Thus, the second method is a quite complex system which is used commonly on many military vessels. When such a vessel wishes to transmit a message to an object which is relatively stationary, it sends the message along with a pulsed signal which gives the ship's exact cycle rate and velocity vector relative to a standard inertial reference point. The receiver then runs the transmission through a computer which decodes the ship's vector information signal (called a DDB for Dynamic Data Burst) and corrects for any distortions. Now, if the stationary receiver wishes to transmit a signal back, it sends out its response in a chopped form fashioned for the ship to read with no computer assistance; that is, unless they have changed their heading, speed, or cycle rate since their initial transmission. The same mechanics apply to two ships using stutterwarp, except the initial message is just the DDB. The receiver ship reads the DDB and alters its cycle rate slightly to mesh with the transmitting ship's. It then sends a confirmation signal that it is ready to receive and meaningful communication can occur."
Essentially, a ship can transmit to a missile, as long as the missile doesn't change course or speed, but the missile cannot transmit back (if it had a transmitter) because it doesn't have the ships vector information, unless the ship isn't maneouvring. Comms are very tight beam and need processing to account for stutterwarp effects.
This is the reason why Triumphant Destiny's flagship stayed back at Beowulf - if stationary it can talk to the ship commanders. However, when USS Columbia made a run at it, it forced the Kafer Delta to spin up the drive and severed fleet communications. All Kafer ships were then individuals.
Note, this might not apply to very short range broadcast comms, but a broadcast rather than tightbeam signal attenuates quickly, and likely needs a lot of power.
The probe will probably work, as long as you aren't under drive...
Passive sensors have no range component. All you have are polar coordinates. You need a range component to resolve a target solution if aiming from the mothership.
However, using proportional navigation, rather simple logic is needed for a collision (as long as the missile can "see"the target), but this isn't great for a bomb-pumped nuke. You'll still need to range for the attack. It would work for a proximity detonation. Given that adjacent range is 100 km on Mongoose a missile will cross this distance in milliseconds. A simple proximity nuke works better, and is potentially far deadlier.
With nuclear weapons in space, there is no blast wave, just a massive burst of X-rays and gamma-rays. Gamma passes through light material doing relatively minor damage (although high doses kill people).* X-rays interact with the electron shells of material, causing explosive effects by flashing matter to a plasma if close enough. A nuke going off 10 m from a ship would instantly destroy it, whereas one 100 m away would only do surface damage and 1 km away would hardly be noticed. Inverse square law...
* 100 Gys, an insta-kill dose would equate to 14 kJ of gamma radiation striking a person, as I calculate
here.
Anyway, the point is that missiles can use the pronav algorithum to strike targets. That's how guided weapons work today - they simply adjust their course so the bearing to the target is constant. That means they're part of a collision triangle and they will intercept. When to explode is handled by a fuse, and the sensor does not need to know the distance, only the bearing.