Electronic – Why does Altium delete the GND vias

It's more complex than this in a lot of occasions because sensitive analogue ground connections may benefit significantly from a local star-pointing regime in isolation to the ground plane with just one solid via-area to the bottom main ground plane.

This is done to avoid inevitable digital currents in the ground plain creating small unwanted digital noise signals between points on the localized analogue "star point system".

Also routing power directly to the most hungry components is also a good idea then, tee-off for the ground plane. Plenty of times I've seen examples of audio amps oscillating because the power tracks have gone to the chip via input connections despite a decent ground plane being used.

On the other hand, with switching regulators, different tactics are used and the main aim would be to group the components that produce a lot of ground current to one area of copper "land" - here I'm thinking of a buck converter where the input capacitor to the chip, the power ground on the chip, the flyback diode ground and the output capacitor ground are star pointed back to the chip's power ground.

This usually prevents upsetting the feedback point from rattling around and you get the expected result of a low noise and well-regulated output.

I'm sure there are other great examples.

You can manually add a net using Design->Netlist->Edit nets, then select each pad and assign that net to it.

But I don't see why you don't want to do this in the schematic.