Nintendo 64 ROMs are often just randomly name (.bin, .z64, n64). It doesn't matter whether you change the extension, as long as the emulator will support the extension, it's good.
There are different formats for N64 ROMs, but I think PJ64 can play them all. If not, use
ToolN64 to swap between the various formats.
For the 64DD games, none have been dumped (at least released) yet. There has just surfaced a system ROM for the 64DD, but that's it.
I don't think emulating the 64DD is the hard part, but dumping the games is.