Even back when the Cave Story port was coming out on WiiWare Nicalis seemed shitty to work with.
Who the hell is going to want to work with them now?
Pixel is still working with them (Cave Story +, Ikachan on DSiWare).
Terry of VVVVVV seems to be okay with his work with them.
They also just announced 8-Bit Fanatics are working with them.
Also, Night Sky is technically Nifflas' game...is he still working with them in any capacity?
I'd say it is more likely the issue with language that has ultimately led the two to communication issues. Example: the tweet. It seems Nigoro was unaware UNTIL the news was public. Was this the case, or was there a message sent to them that was not translated correctly? It's stuff like this we won't know for sure.
As a note, I don't think Tyrone hates Nigoro and is in fact very fond of them...but the fact is WiiWare is dead, it has taken over a year to certify everything, and there is no end in sight. It had to end. But maybe they should have talked it over a bit better...like, say, to a different platform?