C/C++ are considered high/low level languages because you can write fairly high-level code, with complicated data structures and local variables and functions and various other things you'd find in "high"-level languages, and still have it translated into 100% pure uninterpreted assembly language. You can even write freestanding things like bootloaders and operating systems in C/C++ because you can exercise fine control over what external things are needed -- or, more to the point, aren't needed. You can forgo the standard libraries entirely and write code that depends on absolutely nothing.

This is very different from Java where everything has to be fed through an interpreter all the time. It's not the computer's native tongue, so to speak. You couldn't write a bootloader in it -- you'd need something else to load java first. It's not freestanding, not independent.

Your question unfortunately sounds a bit naive. Writing a disk defragmenter isn't trivial -- you need to understand a lot more than the language, you need to understand the structures of the filesystem in question. If you don't know enough about a filesystem to know which sectors to grab to find out what information, you can't write a defragmenter.

They're often written in C/C++, yes. They don't have to be, but because the structures for these filesystems are C/C++ anyway, it may be easiest to use them rather than reinvent the wheel.

If you want to build a defragmenter for educational reasons, I'd suggest working on the MS-DOS FAT16 filesystem which has very simple organization, then working up from there.