I'll try to explain things from a more general perspective.
Many of ZUN's instruments (including the ZUNpet, flute, and the UFO/TD reeds) are from the Edirol SD-90, a hardware sound module from 2001-2. They are rather uncommon and fetch high (~US$550-600) prices on eBay, generally speaking. He also is known to use Groove Agent 3, Virtual Guitarist, and I think some HALion One (eg. pianos) as well for some of the other instruments (pianos, guitars, drums), and uses Cubase as a primary DAW.
No idea of Hiroshige #36's piano, but going by Spaztique's TTS-1 rendition of the latter song it's a heavily layered sound that is quite hard to replicate.
I'll extend the rest of the answer and correction to others, particularly Cubase users as I'm more based in Logic and Sonar, as well as hardware synths (SD-90 owner here).