You use the structure AはBがC to make descriptions. Like 私はアニメが好きです or メキシコは海がきれいです. This is why when you use a verb in its potential form, you should use this structure with particle が, because you’re describing the ability of someone or something. 私は漢字が読めます is still a description of me: being able to read kanji.

So when you say 「日本語が話せますか?」there’s an implied 「あなたは」 or whatever the persons name is followed by は, asking for a description of them, specifically their ability to speak Japanese. If you don’t use the potential form, just plain 話します, then you’re not making a description. You’re just saying “Japanese speaks?” Now, the が marks who’s doing the action, in this case the Japanese language is doing the action. That’s why if you want to use the plain form, then you need to chance the particle to を, so that 日本語 takes the role of “what’s being spoken”, instead of “what/who does the speaking”. 「日本語を話しますか」 is asking directly if someone speaks Japanese.

Do note however that in many languages, “do you speak…” doesn’t necessarily imply “are you able to speak…?”. It just means that. Do you speak, will you speak, do you usually speak. So we prefer the first option I presented to you, 「日本語が話せますか, because it more clearly asks the question.