I've seen the -to variant as well, but I didn't realize that B-N was using it now, as I was specifically told that it was wrong and should be -tsu; I see -tsu on FC-related stuff, but searching for it with -to definitely returns more results. Whether this is a newer shift or not I can't say, although I could have been given misinformation, or it could have been a regional (dialectal) difference.
I honestly wonder if anybody knows anymore how it originated, though I'm pretty sure it means something, and I think someone told me what, once, in the haze of my memory. I certainly don't remember anymore and unless there's some old-timer at N-B to say, I don't know of any way to find out. As Namco is itself a contraction, I wouldn't think they'd just add a single random sound or letter for local branding; I am pretty sure that Namcot was specifically a different division, protected by a different incorporation than the parent Namco.
@ L_E_T: I'll check Famicomplete on the 'Devil World' cart's box for you. As I said, it's all a matter of personal choice. Since this was about Silver-Box' games, but not about 'Silver-Box' pulselines, I included the Robot games in what I'd consider to be part of that set for my own collection. Heck, there's a pile of games that I can include as 'silver box' for subsets. Anyhow, I tend to group my own collection weirdly with many crossover categories.