Reading the story where 'ToSeek's graphic comes from, though does corroborate your information that Gene Roddenberry and the NBC people did in fact see and like the upside down ship model. The story goes on to say that "TV Guide came out, they ran a picture of the ship on the cover, upside down." The TV Guide image that this probably refers to can be seen here (it's not actually a cover, but Matt Jeffries' memory may have been slightly off):
Though as Matt Jefferies goes on to say, that wasn't what he was intending with his wooden model and that it immediately "flopped over, because the birch dowels were heavier! I had an awful time trying to unsell that" to Gene.
As for more ships designed to be upside down, I believe that in many of the spin offs of Star Trek you can see some type of variation of either a saucer or engine tubes. Many of these examples can be found in the Federation Ship Recognition Manual from FASA back in 1985. But while an engine on top of a saucer may 'look' upside down, I believe that the intention is that the crew is still standing 'rightside up'. as the request from Roddenberry was " that we didn't have to worry about gravity" and "wanted" it "to be as practical as possible".
Hope this helps some.
