EndNote has supported Unicode since version 8, but I’m just now getting around to testing it. As long as you activate the appropriate keyboard, Unicode input appears to be fairly straightforward, at least on the Mac (and I assume the PC).
Just a font note – I ended up changing my default in the preferences from Helvetica to Lucida Grande. EndNote does change fonts with script, but Lucida Grande is legible and has a large set of Unicode characters. The equivalent font is ArialUnicode on the PC.
FYI – there may be some quirks for export. See the University of Sydney’s EndNote documentation for details.
One nice feature they point out is the “Translated Author” and “Translated Title” field.

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