The below assumes a robot that can do equal speed cycles for both Hatch Panels and Cargo.
The optimal “for points” strategy is to place cargo in all slots you place hatch panels during sandstorm mode, and null hatch panels on all other locations. Scoring a hatch panel onto a cargo bay with cargo inside is worth 5 points. However, cycles to the cargoship after sandstorm mode starts will only yield 2 points for areas that started with cargo in them, as opposed to 3 points for areas equip with null hatch panels. Thus, to maximize scoring potential, one must only load cargo into areas they can get a hatch panel to in sandstorm mode.
Max Hatch Panels in Auto
It is important to recognize that the maximum number of hatch panels available in sandstorm mode is 5, 3 pre-loaded into each robot and 2 located in the feeder stations. Thus, by the above, an alliance should never have more than 5 cargo balls pre-loaded, and the rest should be null hatch panels.
Game Theory and Hatch Panels
If an alliance has a 50% chance of getting 4 hatch panels instead of 3, then should an alliance preload 3 or 4 cargo? We can use game theory to determine this. If we make the following chart:

We see that is seems that there are no downsides to pre-loading another ball, however, this chart does not account for 2 things. The first is that by preloading a cargo and not scoring the hatch devalues a future cycle. Also, assuming that a robot is capable of scoring a cargo ball instead of a Hatch, then 4 cycles can still be valuable. Our table becomes the following:

By adjusting our percentages, we can find using a similar chart that if there is an equal outcome for an alliance able to score the 4th hatch 33% of the time. Thus, if an alliance has a 33% or higher chance, they should go for the 4th cargo piece.
There are definitely different values one can apply to the above algorithm, so do your own analysis and determine what the probabilities are for your own team.
The Rocket Blues
Can’t quite get that rocket finished in time? It’s possible to slightly increase cycles by preloading cargo near the rocket, and letting it fall out during the match, thus decreasing cycle time to get the cargo in these areas.
Shout of to RoboTigers7892 who spend 20+ minutes waiting for me to reply!