Whether it's good or bad is mostly up to you and your team. Since bootstrap resets most of the styles for the whole document, it's best if your Suitelet doesn't use the native nav menu either or it won't look right, as you've seen. As far as I know, you can basically just upload the bootstrap files to the File Cabinet, then your Suitelet will load and read them from there and write them into the appropriate tags on the page before rendering.