Personally I don't mind this at all as long as emotes don't bring any additional buffs / benefits to the character. I couldn't care less.
I assume Squenix gains something when they collaborate with other companies to generate emotes such as the pizza eating emote and chicken eating emote -- both originally introduced in collaboration with other companies.
They would not be able to release those for free in the future -- that would be unfair to the original paying customers who bought those collaboration items, which also paints the other party in negative light.
Likely there's some legal issues as well in Japan when you do such things. We also don't know what type of contract Squenix had with the companies they collaborated with -- they may be required to provide some sort of payment / download to them... who knows.
In such cases it would make sense for Squenix to charge players for such emotes (only for those that were developed as a part of a collaboration).