Oh huh, I never actually heard that fan theory before. Neat!
If we go with the notion that "Evolution" was in 2366 and ST3 was in 2285 (per the Chronology, anyway), then it's rather imprecise for Data.
Otherwise? That makes more sense than the Enterprise, which had problems, but not a shipwide systemic failure in STV.
I've actually never heard the idea that Data was referring to the Enterprise-A. I don't think that even makes sense, like Dayton Ward has pointed out here.
I think the Excelsior theory was mentioned in the Chronology as a possible explanation for Data's reference in the little "out of universe" section at the end of the entry, and tied it into the conjecture that the Excelsior's transwarp drive failed, and so the project was scrapped (to offer a reason why the Excelsior was using a normal warp drive in the sixth movie, and why normal warp drive was still the engine of choice in the 24th century). The non-canon Haynes guide to the Enterprise chose to state that the Excelsior was the ship that failed and that it was due to transwarp drive malfunctioning.
So far as I know, the connection has yet to be made in canon, although I'm inclined to accept it until we learn otherwise.