Here's why I think Goonies didn't happen on the NES:

1. Konami of America couldn't afford or didn't want to pay the license fee required to Warner Bros. to use their property. This is very likely also why King Kong 2 Ikari no Megaton Punch was never localized. Konami didn't want to pay Universal for the license. (in that case though, the game was substantially better than the film on which it was loosely based)

2. Nintendo of America had at the time a clause in third party licensing agreements that they could only produce five titles for the NES a year. The five games Konami produced on the NES for 1987 were:
Rush'n Attack
Contra
Double Dribble
Castlevania
Gradius

Now assume your Konami. Would it really have made sense to replace one of those games on a game based on a two year old film?

That is what I believe is the bigger reason why Goonies didn't happen on NES. But it did come to North America anyway, as it was in fact a Nintendo Play Choice 10 title.