This is not in relation with Bootstrap nor WordPress themes. It is WordPress related thing and there is nothing you can do about it since many of scripts will always be loaded in header no matter what.
Your website score is much lower because of the following things:
- You don’t have gzip enabled for your webhosting account. This is a must but no shared hosting offers this. However, You can enable gzip using W3 Total Cache which you have enabled but you haven’t configured it at all, which means that it doesn’t do a thing.
- Images are not optimized. You can can use plugin such as WP Smush.it http://wordpress.org/plugins/wp-smushit/ This won’t affect image quality at all but will make your images much smaller.
- Many other things such as (cache expiration) can be set via W3 Total Cache but it requires some knowledge around it.
- Your hosting is nowhere near to be perfect. Shared hosting will never come close to well configured VPS, like I have for my theme demo.
As you can see, there is nothing about the theme since it scored 92 (will improve it slightly with the next update) but your website scores only 47 with the same theme but bad setup.
If you are interested I am open for freelance work to optimized your website, if necessary. However, it is impossible to score over 90 if Pinterest, Twitter, Facebook scripts are used but 80/100 shouldn’t be a problem.