You can see Thulla's escape route on the second level of the Grymforge she jumps into the lake and swims back. Thulla is wearing Thrinn's missing boots, she was taken along with the others before Thrinn sent Gekh to retrieve her. As for how long the gnomes have been digging there, who can say, we do see a pretty sizable pile of corpses, if you want to be morbid, we might be able to judge it by guessing how many gnomes Nere and Thrinn go through in a day.
To be clear, I see no evidence that the gnomes discovered the Grymforge, unless it was a smaller party lead by Wulbren who was looking for the secret of runepowder.
I don't think you want to get too hung up on which and how many entrances to the Underdark there are, also, lining up the maps shouldn't make much sense considering how much distance there is actually travelling downwards, the Underdark is pretty far down isn't it?
You giving the "literal" definition is maybe the problem, we don't always use words in their literal sense, nor is it wrong to call a run down shack decrepit regardless of age. This particular point is becoming a little febrile.
I'm just trying to make sense of it, and to me, the evidence of them finding Grymforge first is that there are more gnome corpses at Grymforge than Decrepit Village as if that's where they were at in greater numbers, Thulla escaped from Grymforge to the Decrepit Village, not vice versa, indicating she was going there to get help, not that it was a place already attacked by duergar that they took gnomes from already, and that the village is unlived in. Search the village. It's a ruins with rotting baskets and buildings decayed with no roofs, broken walls, etc.
And here's something else. Carrion crawler holes on the south side. Hmmm. Now what's that all about? Be a halfling or dwarf and something special happens if you stick your hand inside.
As far as lining up the maps, distance down does not equal distance horizontally. If the Whispering Depths is, let's say, 500 feet east of the temple, if I jump from a cliff in the Depths and drop 1,000 feet down, I shouldn't land somehow 500 feet or more further to the west. But that's what's happening. They literally show you drop from the Whispering Depths into the Underdark.
