How do I find out what processes are accessing the hard disk in a GNU/Linux-based system?

You got three-fifths of the answer right yourself - the one you want is called iotop. Search for it in the extra repositories, it should be there.

htop » F2 » Columns » Active Columns » IO_RATE

Then sort by this column. Also you can add IO_READ_RATE and IO_WRITE_RATE columns and sort according to them.

iotop is the counterpart to top that watches I/O usage information. If you want detailed information on the files opened by a process, or the list of files opened in a directory, or watch over files in the whole system, use lsof.lsof is quite versatile and provides information about open tcp, udp, NFS connections too.

I use atop.

Atop is an ASCII full-screen performance monitor that is capable of reporting the activity of all processes (even if processes have finished during the interval), daily logging of system and process activity for long-term analysis, highlighting overloaded system resources by using colors, etc. At regular intervals, it shows system-level activity related to the CPU, memory, swap, disks and network layers, and for every active process it shows the CPU utilization, memory growth, disk utilization, priority, username, state, and exit code.