I guess it was a meme like this: (https://i1.sndcdn.com/artworks-000117189588-g42qj2-t500x500.jpg) but with this sentence put instead :)
And, actually, tomatoes are not vegetables. Lol!
I would say there's a difference between the scientific meaning of a word and the normal meaning of a word. For example, do you consider an avocado to be a berry? Therefore, I think it's correct both to say that a tomato (or pumpkin, cucumber, etc.) is a fruit and to say that a tomato is a vegetable.
Unfortunately, everyone seems to disagree with me... :)
With time, the difference between both terms blurred and multiple sources consider warzywa and jarzyny as synonyms. Others use the term jarzyny to refer only to those edible plants that are sown in the spring season (jare), harvested in the same year and eaten raw. In contrast warzywa are edible plants that require some thermal processing (uwarzenie).
My 2 cents:
Usually, people consider jarzyny as an ill-defined subset of warzywa, so for simplicity you can use warzywa exclusively and ignore the word jarzyny.
As a native speaker myself, I actually wasn't aware that jarzyny and warzywa are considered different things. People mostly just use them as synonyms. I also asked my mom (also a native speaker of Polish) and she thought they meant the same thing too.
But your conclusion was correct- it's easiest to just use warzywa, and it won't ever be necessary for you to say jarzyny.
So any phrase like this that contains “to” puts the predicate nominative in the nominative, not the insteumental, right? Like, even if you said “Czy pomidor to jest warzywo?” Is that correct? But then if you don’t have the word “to” then it has to be instrumental right? Why does “to” change that?
Well, "to" has several meanings, so that's a bit too much. But you have two constructions to say "X is Y", and the one with "to" puts the following noun phrase in Nominative.
You may read more about it here: https://forum.duolingo.com/comment/16373167
As for "Czy pomidor to jest warzywo?", that is technically correct, but not very common. We don't teach this construction and I believe that (so far) we have only one user that asks for accepting it ;)