I, too, always wondered about this, but never researched it.
Here’s my 2¢:
Namco (sans “t”) = a more internationally-friendly version for branding purposes.
It sounds less-silly to English-speaking audiences, IMHO.
(Like I said, this is my dumbass explanation...I’m ignorant as f*ck on this...I don’t even know what Namcot was supposed to reference, if anything! Ha!)