I do think it is done to go with the rainy season in Japan which usually lasts from June to early/mid July. So the ton of rain should be stopping sometime soon. I know that other Animal Crossing games had the same thing... the only difference is that the rainy season would be announced ahead of time via the bulletin board, but since this is a town that no one has lived on before I suppose Tom Nook/Isabelle wouldn't know that there was going to be a rainy season. I do hope that they add in an update that after you have lived on your island and gone through this once... Tom Nook leaves a warning on the bulletin board ahead of the rainy season.
Either way... I am getting tired of all of this rain. It just stopped on my island right now, but it will probably start back up in like an hour or two... I am starting to get real tired of all of these flowers I am seeing on my island. I wanna clean them up, but I am not going to till I know the rainy season I over.