That basic WiFi implementation merely allows no$gba to run Pokemon (it has a WiFi check immediately when loaded which used to fail and had to be patched out for the game to even run however since this basic implementation that's no longer the case) but it can't do anything practical yet and does not work for the Underground area in Pokemon or any other game or game feature needing WiFi.
If people were able to access the underground it was likely through some sort of cheat, or perhaps they converted and moved their save to the their DS just for that part.