sub- is a derivational prefix, which means that it's generally thought of as attaching below the word level. Adding it to an existing word creates a new word. Compare words like subtotal or subspace. Would you say either of these is more than one word?
The difference here is that subtotal and subspace are established as lexical items, while subaccount is much less established. That is, fewer people are likely to have it in their mental dictionaries, so they'll have to understand it as a combination of sub- and account, and if they can't figure out the proper meaning based on that, someone will have to explain it to them. The reason you can't find it in those dictionaries is because it's less established, not because it consists of more than one word.
I'd say subaccount is a single word.