These .fwt sources aren't recognized as Fan source by F4 and thus displayed as plain text without any syntax highlighting and of course no code completion at all.

That's right, I don't think .fwt files have ever been considered as real Fantom source files.

The only place I've ever seen them is in the JS examples, and I believe that was just to help distinguish between client and server source.

So it's not a convention and it's safe to just use the normal .fan extension?

Exactly - I've never used any other extension!