Datastore script doesn't recognize empty data?

Well, a few things here.

1: You're comparing an empty table, to another empty table. However, you're actually comparing 2 different tables so that will always return false

print({} == {}) -- > false (2 different tables created)

And our empty table isn't nil, so your if statement returns false for both logical operations, which brings us to the the "else" statement. What you wanna do, is check if there's a table, and then check that table and see if anything's inside of it. We can do this easily with the "next" function:

local t = {}

print(next(t)) -- > "nil"

t[1] = "test"

print(next(t)) -- > 1   test

So this would be our revised code:

data = datastore:GetAsync(userId)

-- Making it so if the data is nil, or if it's not nil but it's an empty table, then...

if data == nil or (type(data) == "table" and not next(data)) then
    newkey(userId)
    print("Added user "..userId.." to the index.")
    loginfo("Added "..userId.." to KEY_INDEX at "..os.time())
    --More stuff
else
    for key, value in pairs(data) do
        print(key, "=", value) --It doesn't print anything, so it must be an empty table.
    end
    datastore:SetAsync(userId, data)
    print(userId.." logged on.") --This happens
    loginfo(userId.." logged on at "..os.time())
end

Let me know if you have any questions, hope it helped.