Opening your entire drive as a folder is a bad idea, as you’ve found out.
In order to create the speed of Goto Anything and the tree structure, we keep a “catalogue” of all files and folders added to the tree. Additionally, we listen to filesystem events so we know when files or folders are added, modified or removed.
By adding your entire drive, Sublime Text needs to replicate every file path of your entire drive in memory, and listen to every single filesystem event triggered on every single file and folders. Beyond, that, unless you’ve disabled the Git integration, Sublime Text it opening every git repo on your system, generating a list of ignored files, any changed files and keeping all of that data in memory and watching for updates also.
I highly recommend you check out the project functionality in Sublime Text. You spend 30s or so per project you work on to create a .sublime-project file with the relevant folders. Then you use the quick project switch panel to jump between them. The switch is usually instantaneous and each project keeps track of your open files, previous search terms, etc. Beyond that, when you go to search in files, it defaults to the files in your project instead of your entire hard drive. Indexing should work reasonably, and a whole host of other things will function as expected.