In a 2 layer PCB with a top layer densely populated, from an EMI & EMC point of view should the ground plane be on top, bottom or both and why?
You want as solid ground plane as possible, so you should have the ground on bottom and preferably have no other traces there.

For better copper balance you should also have the copper pours on the top layer to fill the empty spaces. If there isn't any better use for it, connecting the pours to the bottom ground plane with vias is a good choice. Though this has little to no effect on EMC performance.

So from your options the number 3 is the best, but if you are considering only EMC performance the option 2 is practically equally good.

Though, with these questions about 2 layer boards, I always like to remind that nowadays 4 layer boards are cheap, and using 2 layers is recommended only if you have to save every last penny, i.e. you have huge volumes. Otherwise the higher design cost of two layers will outnumber the higher production cost of 4 layers