Hi,
1. If you activate the "group options with product", the option will be added to the cart along with the product and they won't be separated in the cart. So the customers won't be able to remove the main product while leaving the option in the cart.
Also, if you create an unpublished category and have the option product in that category only, the users won't be able to access the product page of the option to add it to the cart separately.
2. There is no option for that. However, there is a hidden mechanism in order to add that capability. Edit the file product / option via the menu Display>Views and add at the beginning the code:
<?php $this->show_option_quantity = true; ?>
That will add a quantity input for each option on the product page.
3. Not at the moment. However, that's a capability which will be in the next version of HikaShop.