Depends on the atmosphere you want to bring I guess. For mystery type of atmosphere, probably I prefer the silent one. But it might be one of the reasons I don't quite much like horror / mystery theme because it "lacks of color". So, music is important for me.
In my game which was heavily focused on battle with minimum to no story at all, one of many things I focused was picking the right battle bgm. I got lot of positive feedback on it. One of my players said that he never get bored of doing battle because he enjoyed the music I picked. To avoid boredom of listening the music though, I rolled 10 battle bgm before the battle, so when you enter the next battle you will be listening to different bgm which it will be refreshing everytime you enter the battle.
My take, for any aspect of the game you constantly visit, or will be staying for so long in there (in my case, I focused on battle), sickness of a BGM can happen, which usually when I do, I mute the game. To pick bgm for this aspect of your game, you have to have a lot of variation of the song. Either you can use a song with long length, or simply just have a lot of song variation to pick.
For sound effect though, it determines the "signature" of your game. Some people tend to refuse to use default SE because their game will be associate to many of RM games, which they don't feel unique. Me though, I use default one because I don't have time picking the right sound effect, I'm already satisfied with default SE, and I don't mind people associate my game as other RM games, because my game is indeed an RM game and I won't deny it.