|My use of Traveller setting and dress falls under|
fair use guidelines for both Mongoose and Far Future Enterprises.
Per rules as written, your only option seems to be "manually load the new projectiles from cargo into the launcher between attack roles during space combat." But given that missile launchers are very low tech weapons, and High Guard has delightful rules on upgrading weapons to make them more versatile, it is easy to derive this:
Ammunition Selector (Double Upgrade): This upgrade changes the linear feed of a missile or sandcaster to that of a loop, allowing the gunner to select and launch specific missiles during the combat turn.
Ammunition Selector (Singe Upgrade): As above, but this reduces ammunition capacity in half due to the space and power requirements for the carousel gears.Now there is nothing stopping you from mixing your missile or cannister types together and using them as necessary.
Of course, this comes with the double drawback of "costs more money" and "if you need a specific type of ammunition, you may not have enough of them due to the mix", but that's the price you pay for flexibility.