Hi,
The problem does not came from Joomla 3.1 but from the template you are using.
The default template of Joomla 3.1 (and 3.0) is bootstrap compatible, like the default backend template of Joomla 3.1
About your breadcrumb question, I do not understand it.
Regards,
Jerome - Obsidev.com
HikaMarket & HikaSerial developer / HikaShop core dev team.
Also helping the HikaShop support team when having some time or couldn't sleep.
By the way, do not send me private message, use the "contact us" form instead.