Well, just in case anyone has the same problem in future and comes looking for a solution, here's how I resolved it.
In System Prefs, go to International, select the Input Menu tab and activate the Devanagari and Devanagari-QWERTY keyboards. Also tick the "show input menu in menu bar" box.
If you then click on the flag in the menu bar and select Devanagari, it will switch devanagari rendering 'on'. You can then use Devanagari MT across the whole platform.
Bizarrely, in some apps (e.g. Text Edit), selecting "Devanagari MT" in the font browser will not render the font as long as you have a different input source selected; but once you select Devanagari as the keyboard layout, then *all* fonts are rendered as Devanagari!
(Amazingly, I spent a couple of hours on the phone with Apple Care and they didn't come up with this simple solution!)