We've not hidden the baskets in our store (yet)... but i suspect it's an attempt to stop the spread. We have antibacterial wipes and hand sanitiser next to the stack of baskets so customers can clean the handle and their hands before they shop.
Plenty of customers do what you do (use their own bag instead of a basket). As a member of floor staff, I'll mention it (you) to the checkouts to double check your bag for life
. But I wouldn't worry about it, it's not uncommon to use your bag instead of basket, and as things are, it's probably more sensible