Why a travel agent? It costs you only (a lot of) extra money. Only in Jakarta are a few travel agents allowed to arrange a visa and then still your parents have to show up at the Netherlands embassy.
Why not directly to the embassy in Jakarta, or to the consulates in Surabaya or Bandung, or to the consular contactpersons in Yogyakarta or Jepara?
Check at www.netherlandsembassy.or.id
Most of the common travel agents cannot arrange a visa for your parents but if they book they (or you) book the tickets there, then definitely they will show you the way to one of these posts.
I wish you success, just take a look at the website of the embassy.