There is no delay in reloading from a population, but it is
1) just because Steve hasn´t gotten around to program a delay in for this and would be gaming the system and
2) micromanagement hell, to manually reload each PDC every time they shoot at something. Generally, I follow the same principles re. PDC magazins as I do with ships and give them enough ammo for 10 to 20 salvos.
Re. assinging missiles to launchers, launchers to firecons, firecons to targets etc.
Battle Control Window (F8) is your friend
You set up one of your ships (missiles/launchers/beams/...), assign PD settings and then hit the "Copy Race" button on the right. This sets up all ships of the same class just like the one you just did.
Similar procedue for assigning targets. Assign target(s) to one of your ships and then hit "Class in TG" or "Class in Sys" to copy the target assignment to every ship of the same class in that task group or in-system.
After that, you hit ""Open Fire" in the "Current Fleet" Area
As for what it was you destroyed, who knows. May you live in interesting times
Re. the divide by zero error. Try turning off orbital movement for asteroids and/or planets and see if it solves things. Other than that, I have no idea.