Shots are not currently saved in sim files. This means saved sim files do not accurately represent the state of the sim with regard to shots when it was saved. This can be critical for debugging shot related problems (they often can't be reproduced from a saved sim file since all the shots are lost in the saved sim). It can also cause unexpected behaviour when sims that are shot dependent are reloaded. For example, the population in a sim where nrg shots last forever and bots have evolved to depend on a high frequency of random nrg shot impacts can crash when initally loaded since the abundance of nrg shots they need tp survive is absent.
Downside? Well, adding shots to saved sims would increase their size proportional to the number of shots. Not sure how much the per shot cost would be, perhaps a few hundred bytes per shot.