This question comes from Chapter 7 of the Order of the Phoenix.
“No, no, it’s not the toilet, it’s the Potter boy’s hearing — they’ve changed the time and venue — it starts at eight o’clock now and it’s down in old Courtroom Ten —”
“Down in old — but they told me — Merlin’s beard —”
I guess Fudge wanted to make the hearing as intimidating as possible for Harry, so this question isn't really about that. From what we know about the Department of Mysteries it seems quite an unlikely place to have a courtroom, whether old or current. The Department of Mysteries is a place where learned wizarding scientists study all aspect of magic at it's deepest and so on. So why have a courtroom there to prosecute alleged crimes?