The Latin indicative is used when a speaker/writer wants to assert a fact about a situation in the real world. The Latin subjunctive is used to describe a situation in the mind that is dependent on something else for its application to reality.
As examples, the reality of the situation could be contingent on some other fact that has implications for the situation's reality, such as a judgement about the fitness of the situation (deliberative subjunctive), someone else's volition (jussive subjunctive), another statement of fact (subjunctive for dependent clauses in indirect statement), or a condition (subjunctive for conditions that are less vivid or contrary to fact).
Imagine you are a Latin speaking cook asked to cook a fish stew. If you see someone with a bag of fish, you might point at the bag and ask the person: "Quot pisces sunt?" You use the indicative, because you are inquiring about a plain fact in the real world.
Now imagine you are cooking for a client who hasn't told you how much stew they want. You might ask: "Quot pisces sint?" You are asking about the desires in the mind of your client, saying "How many fish are there to be?" or "How many fish should there be?" This is the jussive subjunctive.
Suppose you have limited funds and want to send someone to buy as many fish as possible. You hand the person 2 sesterces and wonder how many fish that would/might buy if all of it were used. You might ask: "Quot pisces sint?" "How many fish would there be (if you spent it all)? You are asking about a contingent reality in your mind, not something you are asserting or inquiring about in the real world. This is the subjunctive used in future-less-vivid conditional sentences.
You might look at the guy with the bag of fish and point at the bag with a questioning look. The guy responds by asking you want you want. You could then say "Rogo te quot pisces sint." "I'm asking how many fish there are." Here, the reality of your question depends on the reality of your statement.
The reason for the subjunctive in this case may be harder to square with my generalization, since it seems to talk squarely about a situation in the real world and seems to be equivalent to the straight up question. This equivalence has to with discourse pragmatics and not the actual form of your statement, which is not in the form of a question.
Consider what happens if you make a couple of changes to the sentence. Suppose you say: "Non rogo te quot pisces sint." (I'm not asking you how many fish there are.") In this case, the content of the question is clearly not about the real world, since you are saying the question doesn't actually exist. Suppose you ask: "Rogam te quot pisces sint?" ("Should I ask you how many fish there are?".) (Deliberative subjunctive) Here you don't know whether the question will exist or not, since you are just wondering about its appropriateness. These examples show that merely making the question dependent another statement of reality can make its own reality contingent.
In Latin, using the subjunctive in questions signals that you are merely asking about a situation as it exists in your mind that may or may not correspond to the real world. If you use the indicative, you are inquiring directly about the real world as you perceive it.