What is the best way to bulk update entries?

No. You need to examine all the requests and what exactly increases the time and tweak them more if you want to gain more speed and still update them very often. What DB do you use, mongo, MySQL, postgres? Is it an external db or it is hosted on the same server with strapi?

Yes, inside the find and findone controllers, so the end-users could get a well-formatted response instead of spots__ fields.