From the SEO point of view, the only thing that matters is the final loading speed of your site and related with this, the amount of files you load.
If you are right saying that Bootstrap might be cached, is also true that you can load it from CDN's like MaxCDN and thus getting you one different source of loading when asynchronous sources are important in ...
No effect on SEO AFAIK (assuming they're about comparable in size, caching and parsespeed). About the rest, you need pro's and cons and decide based on that:
- PRO: There is a chance it's cached, granting a quicker load
- PRO: Can save development time with predefined classes and possibilities
- PRO: Can be accessed via exernal load, ...