Perhaps I have not been as clear as I should be. The sequence of counted numbers is infinite, and we would never be able to finish counting all of it. But all we care about for defining ℵ₀ is whether or not the sequence contains some particular value. If it does contain the value, then we can confirm that in finite time, even though the sequence is infinite.
Let me try reframing it a bit. First, you think of some natural number N (e.g., 978) and keep it to yourself. Then, I start counting, "0, 1, 2, 3, 4, 5, ..." and never stop. You listen to me count until you hear N. Then, you can stop listening, even though I'll never stop counting. At that point, you already know that my sequence contains N, and you don't have to keep listening.
I hope you agree that no matter which N you choose, you'll hear me say it sooner or later, as long as I keep counting up by 1. If N is a smaller number, you'll hear me say it sooner; if N is a bigger number, you'll hear me say it later. But there's no N you can choose that forces you to listen to me forever. (And again, just because you stop listening doesn't keep me from talking forever.)
The same thing cannot be done with the real numbers. If you think of some real number R that I don't know, then there's no way for me to count through the real numbers to guarantee that you will eventually hear R and stop listening. Even if I do try to pick a certain sequence, there's a very good chance that you'll never hear R and you'll have to keep listening forever.