I don’t know much about the Mac OS, but in Windows even if you have a huge hard drive if you store too much at C:\ (the root directory) instead of putting it into subdirectories (folders), then Windows will run out of memory to address the “number” of files long before their “size” becomes an issue. It is a fairly huge number, but you probably have a fairly huge number of files, too.
Take a look at the file structure before you delete things. It may only be that you need to set up some folders and move things off the root.
But to answer your starting question, for most of us, most of the time, the “start up drive” is C:\. But on a computer that is set up to enable it, it could also be a D:\ (or other drive letter designator) for the CD drive (such as is required to install an OS on a new computer or hard drive, for example), and there’s no reason other than convention why you can’t still boot from a floppy at A:\ or B:\, if you wanted that for some ungodly reason, like to relive the 1980s or something.