Hi,
1. This indicates that you've turned off the "add to cart legacy" setting of the HikaShop configuration and thus you're using the new add to cart system instead of the old one.
If you turn back off that option, like it is after the update, you will get it working like it was before.
2. There is a setting to configure the duration of the new popup and its size can be changed with CSS. You'll find the options of the new popup in the "HikaShop cart notification" plugin via the Joomla plugins manager.
3. In these settings, you'll also find the possibility to use a real popup, like before (although the popup system will be different). However, I'm afraid you'll have the same issue since the tags won't be processed either.