You really just need to make sure you install it from the meteor node version. You can either sync your system node and npm versions to meteor and then run the command to instlal bcrypt, or you can just make sure you always (even for other modules!) use
meteor npm to install and remove npm modules, and never npm directly.
You may need to remove bcrypt then put it back, though I've found simply reinstalling it correctly fixes up that message every time.
meteor npm uninstall --save bcrypt
meteor npm i -S bcrypt
This goes for yarn too:
meteor npm i -g yarn
meteor yarn add bcrypt