I think the pay-out should be a bit higher.
I think I might have found a resolution to 'Everyone Imports Radioactives' issue. The Third Imperium exports Thorium (for non-weapon fission applications) to the Aslan Heirate, and Tritium to the Florians. The Aslan Heirate (already geared up to produce it for their war on the Glorious Empire) exports Plutonium to both. Someone who wanted to rejigger the prices to account for different amounts of dTons flowing each way could do it by adjusting the prices of these Radioactives.
[Edit:] Also I really like the idea of adjusting the value of the DustSpice in the Treasure ship. Figure all 'Spice' mentioned on the loot tables is black pepper or star anise, or saffron, or whatever, and value that at ~6000 Cr / dTon. MgT 1e Compedium #2, page 66 prices DustSpice at from 500 Cr to 11 kCr per kilogram, but has weirdly low kilograms per dTon -- about 144 kg per dTon, less dense than liquid hydrogen. Using the canon values a dTon of DustSpice is between 72000 Cr and 1584000 Cr per dTon; so the 120 dTons of DustSpice would represent between 8.64 MCr (for the crummy 500 Cr/kg stuff), up to 190.08 MCr for the high-end 11 kCr/kg stuff.
[Edit of the Edit:] I figure that risking a 50/50 destruction / loss of a ~319 MCr ship means the appropriate payout should be similar; maybe higher (why chase 'bad' or just 'even odds' payouts?) which (after the 35 MCr in cash & no-volume valuables) works out to ~9.6 MCr per dTon. If the pirates take the 20 dTons of 'mail' containers (which the ref wants them to do for plot hooks & etc), then either the value of those containers need to rise, or there needs to be ~10 dTons of stuff with a payout around 28.25 MCr/ dTon. [/Edit of the Edit]
If you instead figure that DustSpice is similar in density to Cinnamon, then a 13.5 m^3 dTon is worth right at 3 MCr (for 500 Cr/kg) up to 66.2 MCr (for the highest grade 11 kCr/kg spice). The DustSpice present on the Treasure ship is then worth from 360 MCr to 7944 MCr. In the latter case, it seems to make sense to send naval assets along.
In any case, if the DustSpice is more valuable than the Luxuries, Radioactives, and Pharmaceuticals, then it makes sense to put (~40 dTons of) the highest grade DustSpice in the Vault along with the mail drums, documents, and gemstones. The previous contents of the vault can be shifted to the lower hold. This also fixes the weird '100 dTons in a Vault capable of holding 60 dTons' typo, and helps fix some of the '189 dTons of empty cargo space' issue.
Also note -- it may not be worth the pirates time to steal the Launches. Loaded up with Radioactives, they occupy 20+ dTons of space in the hold, and are only worth 17.43 MCr -- just filling that space with Radioactives (or better) gains the pirates 2.57 MCr more loot. If one can be loaded with valuables and jumped away on an external mount, then that seems worth trying. [/Edit]