“A few seasons later, we learned that Pinkie Pie canonically does have a secret basement under Sugarcube Corner.” Does that mean the writers might have read that fanfic?

Absolutely. The writers of MLP:FiM are very aware of what goes on in the fandom and regularly make nods to it. Hell, the 100th episode, “Slice of Life”, is basically Canonized Fanon: The Episode, a wild ride that celebrates the fandom and the background ponies it has given so much love to.

And then later on there’s “Fame and Misfortune”, by the same writer, in which the Mane Six publish a book about their adventures and everything they’ve learned in the hopes of helping young ponies learn about friendship, only to have the ponies who read it create uproars for all the wrong reasons – flanderizing Pinkie Pie to the point of laughing at everything she says or does, trying to join Applejack’s family, ripping Twilight’s lessons because Rainbow Dash’s are cooler, generally criticizing everything as if it were fictional (”it’s not believable that you would be friends”)… In the end, nothing was resolved (even after this song), but the Mane Six found out they had genuinely helped a few young ponies, and they were happy with that.

Now if that’s not fandom commentary, I don’t know what is.

Anyway, to bring it back to the original question – Pinkie’s secret basement is used for party planning and doesn’t look anything like the place in Cupcakes, for obvious reasons, but yes, I’m 98% sure it was still a reference.