I think it’s all a matter of extent. I think anything really becomes a concern for authority when someone is unfairly profiting from another’s work, exploiting it by means of file-sharing, or copying someone’s work. Transcribing Yoshida Brother pieces would definitely require permission, as it’s a shamisen-specific song.
For pop songs however, I speculate that it’d be more relaxed. It takes time and money to go after people, so I wouldn’t think it’d be worth it for “them” to crack down on a few shamisen enthusiasts wanting to play Poker Face note-for-note on shamisen.
I’m just speculating though.